diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
index 6b50f60d4..b2e408301 100755
--- a/.ci_stuff/test_dag.sh
+++ b/.ci_stuff/test_dag.sh
@@ -184,47 +184,50 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 333 ]; then exit 1 ; fi
 
 # mRNA-seq
 WC=`mRNA-seq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 882 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 879 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 892 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 889 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 908 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 905 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 602 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 599 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 948 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 945 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1005 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1006 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 916 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 913 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 966 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 963 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 807 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 804 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 526 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 523 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 863 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 860 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 920 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 921 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 975 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 972 ]; then exit 1 ; fi
 WC=`mRNA-seq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 657 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`mRNA-seq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 867 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 869 ]; then exit 1 ; fi
 #allelic
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1360 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1357 ]; then exit 1 ; fi
+WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i allelic_BAM_input/filtered_bam --fromBAM --bamExt '.filtered.bam' -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1118 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1367 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1353 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1350 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1367 ]; then exit 1 ; fi
+WC=`mRNA-seq -m allelic-mapping,deepTools_qc,alignment-free -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1803 ]; then exit 1 ; fi
 
-# noncoding-RNA-seq
 WC=`noncoding-RNA-seq -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 717 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index d0200ad21..b6d93a2ce 100755
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.6.1
+  version: 2.7.0
 
 source:
   path: ../
diff --git a/docs/content/News.rst b/docs/content/News.rst
old mode 100755
new mode 100644
index c27fbe4b1..2fbfa886c
--- a/docs/content/News.rst
+++ b/docs/content/News.rst
@@ -1,11 +1,19 @@
 snakePipes News
 ===============
 
+
+snakePipes 2.7.0
+----------------
+
+* Added the allelic version of Salmon-based transcript quantitation to mRNA-seq workflow. Will be run if *both* 'allelic-mapping' and 'alignment-free' modes are specified. An allelic version of sleuth will be run, if sample sheet is provided, as well as DESeq2 on allelic Salmon counts.
+
+
 snakePipes 2.6.1
 ----------------
 
 * Capped tabulate version as 0.9.0 breaks snakemake
 
+
 snakePipes 2.6.0
 ----------------
 
@@ -19,6 +27,7 @@ snakePipes 2.6.0
 * Fixed a couple of issues in the ATAC-seq workflow after sofware versions update.
 * Fixed genome size conversion to string.
 
+
 snakePipes 2.5.4
 ----------------
 
diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
index 574f4077e..766ce2d06 100755
--- a/snakePipes/__init__.py
+++ b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.6.1'
+__version__ = '2.7.0'
diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py
index bcc3f8518..27ee0cbd3 100644
--- a/snakePipes/common_functions.py
+++ b/snakePipes/common_functions.py
@@ -22,6 +22,7 @@ def set_env_yamls():
     return {'CONDA_SHARED_ENV': 'envs/shared.yaml',
             'CONDA_CREATE_INDEX_ENV': 'envs/createIndices.yaml',
             'CONDA_RNASEQ_ENV': 'envs/rna_seq.yaml',
+            'CONDA_SLEUTH_ENV': 'envs/sleuth.yaml',
             'CONDA_RMATS_ENV': 'envs/rMats.yaml',
             'CONDA_scRNASEQ_ENV': 'envs/sc_rna_seq.yaml',
             'CONDA_seurat_ENV': 'envs/sc_rna_seq_seurat.yaml',
diff --git a/snakePipes/shared/rscripts/DESeq2.R b/snakePipes/shared/rscripts/DESeq2.R
index e905633a5..4f76297b1 100755
--- a/snakePipes/shared/rscripts/DESeq2.R
+++ b/snakePipes/shared/rscripts/DESeq2.R
@@ -79,7 +79,7 @@ if(isTRUE(tximport)) {
   tx2gene <- read.delim(tx2gene_file, header = FALSE)
   tx2gene <- tx2gene[c(1,2)]
   # check setup table and import
-  countdata <- checktable(sampleSheet = sampleInfo, salmon_dir = dirname(countFilePath), tx2gene_annot = tx2gene)
+  countdata <- checktable(sampleSheet = sampleInfo, salmon_dir = dirname(countFilePath), tx2gene_annot = tx2gene, alleleSpecific = allelic_info)
 } else {
   sampleInfo$name <- make.names(sampleInfo$name)
   rownames(sampleInfo)<-sampleInfo$name
@@ -93,11 +93,15 @@ if(isTRUE(tximport)) {
 ## ~~~~~~~ 3. run DESeq wrapper ~~~~~~~~
 #in case of the allelic-specific workflow, allow for 1 condition and skip deseq2 basic in this case 
 if(length(unique(sampleInfo$condition))>1){
-    seqout <- DESeq_basic(countdata, coldata = sampleInfo, fdr = fdr, alleleSpecific = allelic_info, from_salmon = tximport)
+    if(tximport & allelic_info){
+        message("Detected allelic Salmon counts. Skipping DESeq_basic.")
+    }else{
+        seqout <- DESeq_basic(countdata, coldata = sampleInfo, fdr = fdr, alleleSpecific = allelic_info, from_salmon = tximport)
 
-    DESeq_writeOutput(DEseqout = seqout,
+        DESeq_writeOutput(DEseqout = seqout,
                 fdr = fdr, outprefix = "DEseq_basic",
                 geneNamesFile = geneNamesFilePath)
+        }
 }
 #DESeq_downstream(DEseqout = seqout, countdata, sampleInfo,
 #             fdr = fdr, outprefix = "DEseq_basic", heatmap_topN = topN,
@@ -105,7 +109,7 @@ if(length(unique(sampleInfo$condition))>1){
 
 ## Run allele-sepecific DESeq wrapper (if asked for)
 if (isTRUE(allelic_info)) {
-    seqout_allelic <- DESeq_allelic(countdata, coldata = sampleInfo, fdr = fdr)
+    seqout_allelic <- DESeq_allelic(countdata, coldata = sampleInfo, fdr = fdr, from_salmon=tximport)
 
     DESeq_writeOutput(DEseqout = seqout_allelic,
                  fdr = fdr, outprefix = "DEseq_allelic",
@@ -132,9 +136,10 @@ write.bibtex(bib, file = 'citations.bib')
 file.copy(rmdTemplate, to = 'DESeq2_report_basic.Rmd')
 
 if(length(unique(sampleInfo$condition))>1){
-  outprefix = "DEseq_basic"
-  cite_options(citation_format = "text",style = "html",cite.style = "numeric",hyperlink = TRUE)
-  render('DESeq2_report_basic.Rmd',
+  if(!tximport & !allelic_info){
+      outprefix = "DEseq_basic"
+      cite_options(citation_format = "text",style = "html",cite.style = "numeric",hyperlink = TRUE)
+      render('DESeq2_report_basic.Rmd',
               output_format = "html_document",
               clean = TRUE,
               params = list(
@@ -142,9 +147,10 @@ if(length(unique(sampleInfo$condition))>1){
                   ddr.df = paste0(outprefix, "_DEresults.tsv"),
                   countdata = countFilePath,
                   coldata = sampleInfo,
-                  fdr = 0.05,
+                  fdr = fdr,
                   heatmap_topN = 20,
                   geneNamesFile = geneNamesFilePath))
+    }
 }
 
 if (isTRUE(allelic_info)) {
@@ -158,7 +164,7 @@ if (isTRUE(allelic_info)) {
                       ddr.df = paste0(outprefix, "_DEresults.tsv"),
                       countdata = countFilePath,
                       coldata = sampleInfo,
-                      fdr = 0.05,
+                      fdr = fdr,
                       heatmap_topN = 20,
                       geneNamesFile = geneNamesFilePath))
 }
diff --git a/snakePipes/shared/rscripts/DESeq2Report.Rmd b/snakePipes/shared/rscripts/DESeq2Report.Rmd
index f54505281..ab647d8b4 100644
--- a/snakePipes/shared/rscripts/DESeq2Report.Rmd
+++ b/snakePipes/shared/rscripts/DESeq2Report.Rmd
@@ -81,7 +81,7 @@ load(params$DEseqoutRdata) ## dds and ddr
 ddr.df <- params$ddr.df  #_DEresults.tsv file
 countdata <- params$countdata
 coldata <- params$coldata
-fdr <- params$fdr
+fdr <- as.numeric(params$fdr)
 heatmap_topN <- params$heatmap_topN
 geneNamesFile <- params$geneNamesFile
 
diff --git a/snakePipes/shared/rscripts/DE_functions.R b/snakePipes/shared/rscripts/DE_functions.R
index 4ca2c5446..2c5320f9a 100644
--- a/snakePipes/shared/rscripts/DE_functions.R
+++ b/snakePipes/shared/rscripts/DE_functions.R
@@ -31,8 +31,13 @@ checktable <- function(countdata = NA, sampleSheet = NA, alleleSpecific = FALSE,
   ## check files
   if(!is.na(salmon_dir)) {
 
-    # mode = Salmon : check whether salmon output files exist in Salmon dir
-    files <- paste0(salmon_dir,"/",sampleSheet$name,".quant.sf")
+    #mode = Salmon : check whether salmon output files exist in Salmon dir
+    if(alleleSpecific){
+        files <- c(paste0(salmon_dir,"/",sampleSheet$name,".genome1.quant.sf"),paste0(salmon_dir,"/",sampleSheet$name,".genome2.quant.sf"))
+    }else{
+        files <- paste0(salmon_dir,"/",sampleSheet$name,".quant.sf")
+    }
+    #files<-dir(salmon_dir,pattern=".quant.sf",full.names=TRUE)
     filecheck <- file.exists(files)
     if(!(all(filecheck == TRUE))) {
       cat("Error! The following File(s) don't exist : ")
@@ -63,7 +68,7 @@ checktable <- function(countdata = NA, sampleSheet = NA, alleleSpecific = FALSE,
         }
     }
   }
-  if(all(is.integer(countdata))){
+  if(all(is.integer(countdata)) | !is.na(salmon_dir)){
         print("All countdata is integer.")
     }else{
         print("Non-integer counts detected. The data will be rounded, as this is well within the expected sampling variation of a technical replicate.")
@@ -88,6 +93,7 @@ DESeq_basic <- function(countdata, coldata, fdr, alleleSpecific = FALSE, from_sa
     cnames.sub<-unique(colnames(coldata)[2:which(colnames(coldata) %in% "condition")])
     d<-as.formula(noquote(paste0("~",paste(cnames.sub,collapse="+"))))
     
+
     # Normal DESeq
     print("Performing basic DESeq: test vs control")
     if(isTRUE(from_salmon)) {
@@ -95,18 +101,18 @@ DESeq_basic <- function(countdata, coldata, fdr, alleleSpecific = FALSE, from_sa
         dds <- DESeq2::DESeqDataSetFromTximport(countdata,
                                   colData = coldata, design =d)
                 
-    } else {
-      print("Using input from count table")
-      if(isTRUE(alleleSpecific)) {
-          rnasamp <- dplyr::select(countdata, dplyr::ends_with("_all"))
-          rownames(coldata)<-colnames(rnasamp)
-          dds <- DESeq2::DESeqDataSetFromMatrix(countData = rnasamp,
-                                    colData = coldata, design =d)
       } else {
-          dds <- DESeq2::DESeqDataSetFromMatrix(countData = countdata,
+          if(isTRUE(alleleSpecific)) {
+            rnasamp <- dplyr::select(countdata, dplyr::ends_with("_all"))
+            rownames(coldata)<-colnames(rnasamp)
+            countdata<-rnasamp
+           }
+
+           dds <- DESeq2::DESeqDataSetFromMatrix(countData = countdata,
                                     colData = coldata, design =d)
+
       }
-    }
+
     if(length(size_factors) > 1) {
         print("applying size factors")
         print(size_factors)
@@ -135,33 +141,50 @@ DESeq_basic <- function(countdata, coldata, fdr, alleleSpecific = FALSE, from_sa
 #'
 #'
 
-DESeq_allelic <- function(countdata, coldata, fdr) {
+DESeq_allelic <- function(countdata, coldata, fdr, from_salmon=FALSE) {
 
     # AlleleSpecific DEseq
     print("Performing Allele-specific DESeq using Interaction design : Genome2 vs Genome1")
+    if(isTRUE(from_salmon)) {
+        # create alleleSpecific design matrix
+        coldata_allelic <- data.frame(name = colnames(as.data.frame(countdata$counts)),
+                   allele = rep(c("genome1", "genome2"), nrow(coldata)),
+                   condition = rep(coldata$condition, each = 2) )
+        rownames(coldata_allelic)<-colnames(as.data.frame(countdata$counts))
+        coldata_allelic$allele<-factor(coldata_allelic$allele,levels=c("genome1","genome2"))
+        coldata_allelic$condition<-factor(coldata_allelic$condition,levels=unique(coldata_allelic$condition))
+        print("Using input from tximport")
+        dds <- DESeq2::DESeqDataSetFromTximport(countdata,
+                                  colData = coldata_allelic, design =~1)
+
+    } else {
+      print("Using input from count table")
     rnasamp <- dplyr::select(countdata, -dplyr::ends_with("_all"))
 
     # create alleleSpecific design matrix
-    design <- data.frame(name = colnames(rnasamp),
+    coldata_allelic <- data.frame(name = colnames(rnasamp),
                    allele = rep(c("genome1", "genome2"), nrow(coldata)),
                    condition = rep(coldata$condition, each = 2) )
-    rownames(design)<-colnames(rnasamp)
+    rownames(coldata_allelic)<-colnames(rnasamp)
+    coldata_allelic$allele<-factor(coldata_allelic$allele,levels=c("genome1","genome2"))
+    coldata_allelic$condition<-factor(coldata_allelic$condition,levels=unique(coldata_allelic$condition))
+    dds <- DESeq2::DESeqDataSetFromMatrix(rnasamp, colData = coldata_allelic,
+                              design = ~1)
+    rownames(dds) <- rownames(rnasamp)
 
+    }
+    
     # Run DESeq
-    if(length(unique(design$condition))>1){
-      dds <- DESeq2::DESeqDataSetFromMatrix(rnasamp, colData = design,
-                              design = ~allele + condition + allele:condition)
-      rownames(dds) <- rownames(rnasamp)
+    if(length(unique(coldata_allelic$condition))>1){
+      DESeq2::design(dds) <- formula(~allele + condition + allele:condition)
       dds <- DESeq2::DESeq(dds,betaPrior = FALSE)
       ddr <- DESeq2::results(dds, name=paste0("allelegenome2.condition",unique(coldata$condition)[2]))
       ddr_shrunk <- DESeq2::lfcShrink(dds,coef=paste0("allelegenome2.condition",unique(coldata$condition)[2]),type="apeglm",res=ddr)
     } else {
-    dds <- DESeq2::DESeqDataSetFromMatrix(rnasamp, colData = design,
-                              design = ~allele)
-      rownames(dds) <- rownames(rnasamp)
-      dds <- DESeq2::DESeq(dds,betaPrior = FALSE)
-      ddr <- DESeq2::results(dds, name="allele_genome2_vs_genome1")
-      ddr_shrunk <- DESeq2::lfcShrink(dds,coef="allele_genome2_vs_genome1",type="apeglm",res=ddr)
+        DESeq2::design(dds) <- formula(~allele)
+        dds <- DESeq2::DESeq(dds,betaPrior = FALSE)
+        ddr <- DESeq2::results(dds, name="allele_genome2_vs_genome1")
+        ddr_shrunk <- DESeq2::lfcShrink(dds,coef="allele_genome2_vs_genome1",type="apeglm",res=ddr)
     }
     output <- list(dds = dds, ddr = ddr, ddr_shrunk=ddr_shrunk)
     return(output)
diff --git a/snakePipes/shared/rscripts/sleuth.R b/snakePipes/shared/rscripts/sleuth.R
index 3c26b6ad4..23f4c3bfa 100644
--- a/snakePipes/shared/rscripts/sleuth.R
+++ b/snakePipes/shared/rscripts/sleuth.R
@@ -38,9 +38,7 @@ print(salmon_dirs)
 
 s2c = mutate(sample_info, path=salmon_dirs)
 ## reorder conditions (for Wald test later on: order of comparison important for fold change)
-if ( s2c$condition[[1]] != levels(s2c$condition)[[1]] ) {
-  s2c$condition =  relevel(s2c$condition, as.character(s2c$condition[[1]]) )
-}
+s2c$condition<-factor(s2c$condition,levels=unique(s2c$condition))
 print(s2c)
 
 ## get gene names / symbol names
@@ -50,10 +48,12 @@ if (exists('t2g')) {
   colnames(t2g) <- c("target_id","ens_gene","ext_gene")
 
   ## add gene names
-  so <- sleuth_prep(s2c, full_model=d, target_mapping = t2g)
+  so <- sleuth_prep(s2c, full_model=d, target_mapping = t2g, num_cores=6,
+        transformation_function=function(x) log2(x + 0.5))
 } else {
   ## construct sleuth object
-  so = sleuth_prep(s2c, full_model=d)
+  so = sleuth_prep(s2c, full_model=d, num_cores=6,
+        transformation_function=function(x) log2(x + 0.5))
 }
 
 ## model expression responding on condition
diff --git a/snakePipes/shared/rscripts/sleuth_allelic.R b/snakePipes/shared/rscripts/sleuth_allelic.R
new file mode 100644
index 000000000..c88c5a0c6
--- /dev/null
+++ b/snakePipes/shared/rscripts/sleuth_allelic.R
@@ -0,0 +1,123 @@
+.libPaths(R.home("library"))
+
+library("sleuth")
+library("dplyr")
+#library("biomaRt")
+
+args = commandArgs(trailingOnly=TRUE)
+
+## Debug only !!!
+## t2g_file = "snakemake_workflows/shared/organisms/dm6.t2g"
+## sample_info_file = "sampleSheet.tsv"
+## indir = "Salmon"
+## outdir = "sleuth"
+
+sample_info_file = args[[1]]
+indir = args[[2]]
+outdir = args[[3]]
+fdr = args[[4]]
+t2g_file = args[[5]]
+
+setwd(outdir)
+
+sample_info = read.table(sample_info_file, header=T)#[,1:2]
+coldata_allelic <- data.frame(name = paste0(rep(sample_info$name,each=2),c(".genome1",".genome2")),
+                   allele = rep(c("genome1", "genome2"), nrow(sample_info)),
+                   condition = rep(sample_info$condition, each = 2) )
+coldata_allelic$allele<-factor(coldata_allelic$allele,levels=c("genome1","genome2"))
+coldata_allelic$condition<-factor(coldata_allelic$condition,levels=unique(coldata_allelic$condition))
+sample_info<-coldata_allelic
+
+if(length(unique(sample_info$condition))>1){
+message("Fitting full model with allele, condition and allele:condition.")
+    d<-formula(~allele + condition + allele:condition)
+#    d0<-formula(~allele + condition)
+}else{
+message("Fitting full model with allele only.")
+    d<-formula(~allele)
+#    d0<-formula(~1)
+}
+colnames(sample_info)[colnames(sample_info) %in% "name"] ="sample"
+print(sample_info)
+sample_info$sample
+
+sample_id = list.dirs(file.path(indir), recursive=F, full.names=F)
+sample_id = sort(sample_id[grep('[^benchmark][^SalmonIndex]', sample_id, invert=F)])
+print(sample_id)
+#sample_id = intersect(sample_info$sample, sample_id) # get only those sample that are defined in the sampleInfo!
+sample_id<-sample_id[match(sample_info$sample,sample_id)]
+print(sample_id)
+
+salmon_dirs = sapply(sample_id, function(id) file.path(indir, id))
+print(salmon_dirs)
+
+s2c = mutate(sample_info, path=salmon_dirs)
+## reorder conditions (for Wald test later on: order of comparison important for fold change)
+s2c$condition<-factor(s2c$condition)
+if ( s2c$condition[[1]] != levels(s2c$condition)[[1]] ) {
+  s2c$condition =  relevel(s2c$condition, as.character(s2c$condition[[1]]) )
+}
+print(s2c)
+
+## get gene names / symbol names
+tryCatch( { t2g = read.table(t2g_file, header=F) },error = function(e) { print('No t2g file available!') },finally = {})
+
+if (exists('t2g')) {
+  colnames(t2g) <- c("target_id","ens_gene","ext_gene")
+
+  ## add gene names
+  so <- sleuth_prep(s2c, full_model=d, target_mapping = t2g, num_cores=6,
+                  transformation_function = function(x) log2(x + 0.5))
+} else {
+  ## construct sleuth object
+  so = sleuth_prep(s2c, full_model=d, num_cores=6,
+                  transformation_function = function(x) log2(x + 0.5))
+}
+
+## model expression responding on condition
+so = sleuth_fit(so)
+#so <- sleuth_fit(so, d, 'full')
+#so <- sleuth_fit(so, d0, 'reduced')
+
+
+# ## fit reduced model (not depending on any factor)
+# so <- sleuth_fit(so, ~1, 'reduced')
+#
+# ## likelihood ratio test (LRT) between models to get transcripts affected by condition.
+# ## Usually considered more stringent than Wald test. No fold change!
+# so <- sleuth_lrt(so, 'reduced', 'full')
+# results_table_lrt <- sleuth_results(so, 'reduced:full', test_type = 'lrt')
+# head(results_table_lrt)
+
+## Wald test (to get *fold change*)
+if(length(unique(sample_info$condition))>1){
+    wald_beta_name = paste0("allelegenome2:condition",unique(coldata_allelic$condition)[2])
+}else{
+    wald_beta_name = "allelegenome2"
+}
+so <- sleuth_wt(so, wald_beta_name, "full")
+results_table_wt <- sleuth_results(so, wald_beta_name)
+head(results_table_wt)
+write.table(results_table_wt, "Wald-test.results.tsv", col.names=T, row.names=F, quote=F, sep="\t")
+#so <- sleuth_lrt(so, 'reduced', 'full')
+#results_table_lrt <- sleuth_results(so, 'reduced:full', test_type = 'lrt')
+#write.table(results_table_lrt, "LRT-test.results.tsv", col.names=T, row.names=F, quote=F, sep="\t")
+
+## view fitted models and tests
+models(so)
+tests(so)
+
+saveRDS(so, file='so.rds')
+so = readRDS("so.rds")
+
+write(c("library(sleuth)",
+        "so = readRDS('so.rds')",
+        "sleuth_live(so)"),
+      file="sleuth_live.R")
+
+pdf("MA-plot.pdf")
+plot_ma(so, wald_beta_name, sig_level = fdr)
+dev.off()
+
+
+# sleuth_live(so, "wt") # wt for Wald test
diff --git a/snakePipes/shared/rules/DESeq2.multipleComp.snakefile b/snakePipes/shared/rules/DESeq2.multipleComp.snakefile
index 4f3030179..f6365f469 100644
--- a/snakePipes/shared/rules/DESeq2.multipleComp.snakefile
+++ b/snakePipes/shared/rules/DESeq2.multipleComp.snakefile
@@ -54,7 +54,7 @@ rule DESeq2:
 
 
 ## DESeq2 (on Salmon)
-rule DESeq2_Salmon:
+rule DESeq2_Salmon_basic:
     input:
         counts_table = "Salmon/counts.transcripts.tsv",
         sampleSheet = lambda wildcards: checkpoints.split_sampleSheet.get(compGroup=wildcards.compGroup).output,
diff --git a/snakePipes/shared/rules/DESeq2.singleComp.snakefile b/snakePipes/shared/rules/DESeq2.singleComp.snakefile
index 7939f7961..6216aefbf 100644
--- a/snakePipes/shared/rules/DESeq2.singleComp.snakefile
+++ b/snakePipes/shared/rules/DESeq2.singleComp.snakefile
@@ -41,7 +41,7 @@ rule DESeq2:
 
 
 ## DESeq2 (on Salmon)
-rule DESeq2_Salmon:
+rule DESeq2_Salmon_basic:
     input:
         counts_table = "Salmon/counts.transcripts.tsv",
         sampleSheet = sampleSheet,
@@ -75,3 +75,38 @@ rule DESeq2_Salmon:
         "../{input.tx2gene_file} " # 7
         "{params.rmdTemplate} " # 8
         " > ../{log.out} 2> ../{log.err}"
+
+rule DESeq2_Salmon_allelic:
+    input:
+        counts_table = "SalmonAllelic/counts.transcripts.tsv",
+        sampleSheet = sampleSheet,
+        tx2gene_file = "Annotation/genes.filtered.t2g",
+        symbol_file = "Annotation/genes.filtered.symbol" #get_symbol_file
+    output:
+        "{}/DESeq2.session_info.txt".format(get_outdir("DESeq2_SalmonAllelic",sampleSheet))
+    log:
+        out = "{}/logs/DESeq2.out".format(get_outdir("DESeq2_SalmonAllelic",sampleSheet)),
+        err = "{}/logs/DESeq2.err".format(get_outdir("DESeq2_SalmonAllelic",sampleSheet))
+    benchmark:
+        "{}/.benchmark/DESeq2.SalmonAllelic.benchmark".format(get_outdir("DESeq2_SalmonAllelic",sampleSheet))
+    params:
+        script=os.path.join(maindir, "shared", "rscripts", "DESeq2.R"),
+        outdir = get_outdir("DESeq2_SalmonAllelic",sampleSheet),
+        fdr = 0.05,
+        importfunc = os.path.join(maindir, "shared", "rscripts", "DE_functions.R"),
+        allele_info = 'TRUE',
+        tx2gene_file = "Annotation/genes.filtered.t2g",
+        rmdTemplate = os.path.join(maindir, "shared", "rscripts", "DESeq2Report.Rmd")
+    conda: CONDA_RNASEQ_ENV
+    shell:
+        "cd {params.outdir} && "
+        "Rscript {params.script} "
+        "{input.sampleSheet} " # 1
+        "../{input.counts_table} " # 2
+        "{params.fdr} " # 3
+        "../{input.symbol_file} " # 4
+        "{params.importfunc} " # 5
+        "{params.allele_info} " # 6
+        "../{input.tx2gene_file} " # 7
+        "{params.rmdTemplate} " # 8
+        " > ../{log.out} 2> ../{log.err}"
diff --git a/snakePipes/shared/rules/SNPsplit.snakefile b/snakePipes/shared/rules/SNPsplit.snakefile
index d8107d883..37169ab55 100644
--- a/snakePipes/shared/rules/SNPsplit.snakefile
+++ b/snakePipes/shared/rules/SNPsplit.snakefile
@@ -19,7 +19,7 @@ if aligner == "Bowtie2":
             "SNPsplit {params.pairedEnd}"
             " -o {params.outdir} --snp_file {input.snp} {input.bam} 2> {log}"
 
-elif aligner == "STAR":
+elif aligner == "STAR" or aligner == "EXTERNAL_BAM":
     rule snp_split:
         input:
             snp = SNPFile,
diff --git a/snakePipes/shared/rules/Salmon_allelic.snakefile b/snakePipes/shared/rules/Salmon_allelic.snakefile
new file mode 100755
index 000000000..ed4df369b
--- /dev/null
+++ b/snakePipes/shared/rules/Salmon_allelic.snakefile
@@ -0,0 +1,170 @@
+allelic_suffix = ['genome1', 'genome2']
+
+## Salmon Index
+
+rule SalmonIndex:
+    input:
+        "Annotation/genes.filtered.fa",
+        genome_fasta
+    output:
+        "Salmon/SalmonIndex/decoys.txt",
+        temp("Salmon/SalmonIndex/seq.fa"),
+        "Salmon/SalmonIndex/seq.bin"
+    benchmark:
+        "Salmon/.benchmark/Salmon.index.benchmark"
+    params:
+        salmonIndexOptions = salmonIndexOptions
+    log:
+        out = "Salmon/SalmonIndex/SalmonIndex.out",
+        err = "Salmon/SalmonIndex/SalmonIndex.err",
+    threads: lambda wildcards: 16 if 16<max_thread else max_thread
+    conda: CONDA_RNASEQ_ENV
+    shell: """
+        grep "^>" {input[1]} | cut -d " " -f 1 | tr -d ">" > {output[0]}
+        cat {input[0]} {input[1]} > {output[1]}
+        salmon index -p {threads} -t {output[1]} -d {output[0]} -i Salmon/SalmonIndex {params.salmonIndexOptions} > {log.out} 2> {log.err}
+        """
+
+
+def getSalmon_libtype(pairedEnd, libraryType):
+    """
+    Convert from a featureCounts library type to a HISAT2 option string
+    """
+    if pairedEnd:
+        if libraryType == 1:
+            return "ISF"
+        elif libraryType == 2:
+            return "ISR"
+        else:
+            return "IU"
+    else:
+        if libraryType == 1:
+            return "SF"
+        elif libraryType == 2:
+            return "SR"
+        else:
+            return "U"
+
+## Salmon quant, the bootstraps are needed in Sleuth
+if pairedEnd:
+    rule getAllelicFQ:
+        input:
+            allelic_bam="allelic_bams/{sample}.{allelic_suffix}.sorted.bam",
+            allelic_bai="allelic_bams/{sample}.{allelic_suffix}.sorted.bam.bai"
+        output:
+            r1="allelicFASTQ/{sample}.{allelic_suffix}_R1.fastq.gz",
+            r2="allelicFASTQ/{sample}.{allelic_suffix}_R2.fastq.gz"
+        log: "allelicFASTQ/logs/bam2fq.{sample}.{allelic_suffix}.log"
+        benchmark: "allelicFASTQ/.benchmark/bam2fq.{sample}.{allelic_suffix}.benchmark"
+        threads: 4
+        conda: CONDA_SHARED_ENV
+        shell: """
+               samtools collate -@ {threads} -u -O {input.allelic_bam} | \\
+samtools fastq -1 {output.r1} -2 {output.r2} -0 /dev/null -s /dev/null -n  \\
+                2> {log}
+                """
+    rule SalmonQuant:
+        input:
+            r1 = "allelicFASTQ/{sample}.{allelic_suffix}_R1.fastq.gz",
+            r2 = "allelicFASTQ/{sample}.{allelic_suffix}_R2.fastq.gz",
+            bin = "Salmon/SalmonIndex/seq.bin"
+        output:
+            quant = "SalmonAllelic/{sample}.{allelic_suffix}/quant.sf"
+        log: "SalmonAllelic/logs/{sample}.{allelic_suffix}.quant.log"
+        benchmark:
+            "SalmonAllelic/.benchmark/SalmonQuant.{sample}.{allelic_suffix}.benchmark"
+        params:
+            outdir = "SalmonAllelic/{sample}.{allelic_suffix}",
+            gtf = genes_gtf,
+            lib_type = getSalmon_libtype(pairedEnd, libraryType)
+        threads: 8
+        conda: CONDA_RNASEQ_ENV
+        shell: """
+            salmon quant -p {threads} --softclipOverhangs --validateMappings --numBootstraps 50 -i Salmon/SalmonIndex -l {params.lib_type} -1 {input.r1} -2 {input.r2} -o {params.outdir} 2> {log}
+            """
+else:
+    rule getAllelicFQ:
+        input:
+            allelic_bam="allelic_bams/{sample}.{allelic_suffix}.sorted.bam",
+            allelic_bai="allelic_bams/{sample}.{allelic_suffix}.sorted.bam.bai"
+        output:
+            r1="allelicFASTQ/{sample}.{allelic_suffix}_R1.fastq.gz"
+        log: "allelicFASTQ/logs/bam2fq.{sample}.{allelic_suffix}.log"
+        benchmark: "allelicFASTQ/.benchmark/bam2fq.{sample}.{allelic_suffix}.benchmark"
+        threads: 4
+        conda: CONDA_SHARED_ENV
+        shell: """
+            samtools collate -@ {threads} -u -O {input.allelic_bam} | \\
+samtools fastq -1 /dev/null -2 /dev/null -0 /dev/null -s {output.r1} -n  \\
+                2> {log}
+                """
+    rule SalmonQuant:
+        input:
+            fastq = "allelicFASTQ/{sample}.{allelic_suffix}_R1.fastq.gz",
+            bin = "SalmonAllelic/SalmonIndex/seq.bin",
+        output:
+            quant = "SalmonAllelic/{sample}.{allelic_suffix}/quant.sf"
+        log: "SalmonAllelic/logs/{sample}.{allelic_suffix}.quant.log"
+        benchmark:
+            "SalmonAllelic/.benchmark/SalmonQuant.{sample}.{allelic_suffix}.benchmark"
+        params:
+            outdir = "SalmonAllelic/{sample}.{allelic_suffix}",
+            gtf = genes_gtf,
+            lib_type = getSalmon_libtype(pairedEnd, libraryType)
+        threads: 8
+        conda: CONDA_RNASEQ_ENV
+        shell: """
+            salmon quant -p {threads} --softclipOverhangs --validateMappings --numBootstraps 50 -i Salmon/SalmonIndex -l {params.lib_type} -r {input.fastq} -o {params.outdir} 2> {log}
+            """
+
+
+rule Salmon_symlinks:
+    input:
+        quant = "SalmonAllelic/{sample}.{allelic_suffix}/quant.sf"
+    output:
+        quant = "SalmonAllelic/{sample}.{allelic_suffix}.quant.sf"
+    shell: """
+         ln -s ../{input.quant} {output.quant}
+            """
+
+
+rule Salmon_TPM:
+    input:
+        expand("SalmonAllelic/{sample}.{allelic_suffix}.quant.sf", sample=samples,allelic_suffix=allelic_suffix)
+    output:
+        "SalmonAllelic/TPM.transcripts.tsv"
+    benchmark:
+        "SalmonAllelic/.benchmark/Salmon_TPM.benchmark"
+    log:
+        "SalmonAllelic/logs/Salmon_TPM.log"
+    conda: CONDA_RNASEQ_ENV
+    shell:
+        "Rscript "+os.path.join(maindir, "shared", "rscripts", "merge_count_tables.R")+" Name TPM {output} {input} "
+
+
+rule Salmon_counts:
+    input:
+        expand("SalmonAllelic/{sample}.{allelic_suffix}.quant.sf", sample=samples,allelic_suffix=allelic_suffix)
+    output:
+        "SalmonAllelic/counts.transcripts.tsv"
+    benchmark:
+        "SalmonAllelic/.benchmark/Salmon_counts.benchmark"
+    log:
+        "SalmonAllelic/logs/Salmon_counts.log"
+    conda: CONDA_RNASEQ_ENV
+    shell:
+        "Rscript "+os.path.join(maindir, "shared", "rscripts", "merge_count_tables.R")+" Name NumReads {output} {input} "
+
+
+## Prepare Salmon output for Sleuth
+rule Salmon_wasabi:
+    input:
+        "SalmonAllelic/{sample}.{allelic_suffix}.quant.sf"
+    output:
+        "SalmonAllelic/{sample}.{allelic_suffix}/abundance.h5"
+    log: "SalmonAllelic/logs/{sample}.{allelic_suffix}.wasabi.log"
+    params:
+        "SalmonAllelic/{sample}.{allelic_suffix}/"
+    conda: CONDA_RNASEQ_ENV
+    shell:
+        "Rscript "+os.path.join(maindir, "shared", "rscripts", "wasabi.R")+" {params} 2> {log}"
diff --git a/snakePipes/shared/rules/envs/rna_seq.yaml b/snakePipes/shared/rules/envs/rna_seq.yaml
index 4882f36ed..db4437bb7 100755
--- a/snakePipes/shared/rules/envs/rna_seq.yaml
+++ b/snakePipes/shared/rules/envs/rna_seq.yaml
@@ -12,7 +12,6 @@ dependencies:
  - salmon = 1.9.0
  - r-base = 4.1.3
  - r-wasabi
- - r-sleuth
  - r-dplyr
  - r-ggplot2
  - r-pheatmap
diff --git a/snakePipes/shared/rules/envs/sleuth.yaml b/snakePipes/shared/rules/envs/sleuth.yaml
new file mode 100755
index 000000000..6c504b2aa
--- /dev/null
+++ b/snakePipes/shared/rules/envs/sleuth.yaml
@@ -0,0 +1,8 @@
+name: snakepipes_sleuth_environment_2.0
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - r-base = 4.2.0
+ - r-sleuth = 0.30.1
+ - r-dplyr
diff --git a/snakePipes/shared/rules/multiQC.snakefile b/snakePipes/shared/rules/multiQC.snakefile
index cfe1ca21e..96cfeb229 100755
--- a/snakePipes/shared/rules/multiQC.snakefile
+++ b/snakePipes/shared/rules/multiQC.snakefile
@@ -81,8 +81,12 @@ def multiqc_input_check(return_value):
             infiles.append( expand("allelic_bams/{sample}.SNPsplit_sort.yaml", sample = samples) )
             indir += "allelic_bams"
         if "alignment-free" in mode:
-            infiles.append( expand("Salmon/{sample}/quant.sf", sample = samples) )
-            indir += " Salmon "
+            if "allelic-mapping" in mode:
+                infiles.append( expand("SalmonAllelic/{sample}.{allelic_suffix}/quant.sf", sample = samples,allelic_suffix=allelic_suffix) )
+                indir += " SalmonAllelic "
+            else:
+                infiles.append( expand("Salmon/{sample}/quant.sf", sample = samples) )
+                indir += " Salmon "
     elif pipeline == "noncoding-rna-seq":
         infiles.append(expand("deepTools_qc/estimateReadFiltering/{sample}_filtering_estimation.txt",sample=samples))
         indir += " STAR deepTools_qc "
diff --git a/snakePipes/shared/rules/sleuth.multiComp.snakefile b/snakePipes/shared/rules/sleuth.multiComp.snakefile
index 58661d6a9..3f1b9c7cb 100644
--- a/snakePipes/shared/rules/sleuth.multiComp.snakefile
+++ b/snakePipes/shared/rules/sleuth.multiComp.snakefile
@@ -17,11 +17,12 @@ rule sleuth_Salmon:
         indir = os.path.join(outdir,"Salmon"),
         outdir = os.path.join(outdir,"sleuth_Salmon_{}".format(os.path.splitext(os.path.basename(str(sampleSheet)))[0]+".{compGroup}")),
         sampleSheet = lambda wildcards,input: os.path.join(outdir,str(input.sampleSheet)),
-        fdr = 0.05,
+        fdr = 0.05
+    threads: 6
     log:
         out = "sleuth_Salmon_{}/logs/sleuth.out".format(os.path.splitext(os.path.basename(str(sampleSheet)))[0]+".{compGroup}"),
         err = "sleuth_Salmon_{}/logs/sleuth.err".format(os.path.splitext(os.path.basename(str(sampleSheet)))[0]+".{compGroup}")
-    conda: CONDA_RNASEQ_ENV
+    conda: CONDA_SLEUTH_ENV
     shell:
         "Rscript {params.script} "
         "{params.sampleSheet} "
diff --git a/snakePipes/shared/rules/sleuth.singleComp.snakefile b/snakePipes/shared/rules/sleuth.singleComp.snakefile
index e14afb944..8b4c53644 100644
--- a/snakePipes/shared/rules/sleuth.singleComp.snakefile
+++ b/snakePipes/shared/rules/sleuth.singleComp.snakefile
@@ -15,11 +15,39 @@ rule sleuth_Salmon:
         script=os.path.join(maindir, "shared", "rscripts", "sleuth.R"),
         indir = os.path.join(outdir,"Salmon"),
         outdir = os.path.join(outdir,"sleuth_Salmon_{}".format(sample_name)),
-        fdr = 0.05,
+        fdr = 0.05
+    threads: 6
     log:
         out = "sleuth_Salmon_{}/logs/sleuth.out".format(sample_name),
         err = "sleuth_Salmon_{}/logs/sleuth.err".format(sample_name)
-    conda: CONDA_RNASEQ_ENV
+    conda: CONDA_SLEUTH_ENV
+    shell:
+        "Rscript {params.script} "
+        "{input.sampleSheet} "
+        "{params.indir} "
+        "{params.outdir} "
+        "{params.fdr} " + os.path.join(outdir,"{input.t2g}") +
+        " >{log.out} 2>{log.err}"
+
+rule sleuth_SalmonAllelic:
+    input:
+        quant_files = expand("SalmonAllelic/{sample}.{allele}/abundance.h5", sample=samples,allele=["genome1","genome2"]),
+        t2g = "Annotation/genes.filtered.t2g",
+        sampleSheet = sampleSheet
+    output:
+        "sleuth_SalmonAllelic_{}/so.rds".format(sample_name)
+    benchmark:
+        "sleuth_SalmonAllelic_{}/.benchmark/sleuth.Salmon.benchmark".format(sample_name)
+    params:
+        script=os.path.join(maindir, "shared", "rscripts", "sleuth_allelic.R"),
+        indir = os.path.join(outdir,"SalmonAllelic"),
+        outdir = os.path.join(outdir,"sleuth_SalmonAllelic_{}".format(sample_name)),
+        fdr = 0.05
+    threads: 6
+    log:
+        out = "sleuth_SalmonAllelic_{}/logs/sleuth.out".format(sample_name),
+        err = "sleuth_SalmonAllelic_{}/logs/sleuth.err".format(sample_name)
+    conda: CONDA_SLEUTH_ENV
     shell:
         "Rscript {params.script} "
         "{input.sampleSheet} "
diff --git a/snakePipes/workflows/mRNA-seq/Snakefile b/snakePipes/workflows/mRNA-seq/Snakefile
index baf145378..f48af4223 100755
--- a/snakePipes/workflows/mRNA-seq/Snakefile
+++ b/snakePipes/workflows/mRNA-seq/Snakefile
@@ -71,27 +71,39 @@ if not fromBAM:
         include: os.path.join(maindir, "shared", "rules", "SNPsplit.snakefile")
         # deepTools QC
         include: os.path.join(maindir, "shared", "rules", "deepTools_RNA_allelic.snakefile")
+        if "alignment-free" in mode:
+            include: os.path.join(maindir, "shared", "rules", "Salmon_allelic.snakefile")
+            include: os.path.join(maindir, "shared", "rules", "sleuth.singleComp.snakefile")
+#            include: os.path.join(maindir, "shared", "rules", "DESeq2.singleComp.snakefile")
     else:
         # HISAT2/STAR
         include: os.path.join(maindir, "shared", "rules", "RNA_mapping.snakefile")
-
-    ## Salmon
-    if "alignment-free" in mode:
-        include: os.path.join(maindir, "shared", "rules", "Salmon.snakefile")
-        ## Sleuth (on Salmon)
-        if sampleSheet:
-            if isMultipleComparison:
-                include: os.path.join(maindir, "shared", "rules", "sleuth.multiComp.snakefile")
-            else:
-                include: os.path.join(maindir, "shared", "rules", "sleuth.singleComp.snakefile")
+        ## Salmon
+        if "alignment-free" in mode:
+            include: os.path.join(maindir, "shared", "rules", "Salmon.snakefile")
+            ## Sleuth (on Salmon)
+            if sampleSheet:
+                if isMultipleComparison:
+                    include: os.path.join(maindir, "shared", "rules", "sleuth.multiComp.snakefile")
+                else:
+                    include: os.path.join(maindir, "shared", "rules", "sleuth.singleComp.snakefile")
 
 else:
     fastqc=False
     trim=False
     downsample=None
+    if "allelic-mapping" in mode:
+        allele_mode = "from_bam"
+        star_index_allelic = NMaskedIndex
+        SNPFile = SNPfile
+        # SNPsplit
+        include: os.path.join(maindir, "shared", "rules", "SNPsplit.snakefile")
+        # deepTools QC
+        include: os.path.join(maindir, "shared", "rules", "deepTools_RNA_allelic.snakefile")
 
     include: os.path.join(maindir, "shared", "rules", "LinkBam.snakefile")
 
+
 if "allelic-mapping" in mode:
     ## featureCounts_allelic
     include: os.path.join(maindir, "shared", "rules", "featureCounts_allelic.snakefile")
@@ -107,7 +119,7 @@ include:os.path.join(maindir, "shared", "rules", "RNA-seq_qc_report.snakefile")
 
 ## DESeq2
 if sampleSheet:
-    if isMultipleComparison:
+    if isMultipleComparison and not "allelic-mapping" in mode:
         include: os.path.join(maindir, "shared", "rules", "DESeq2.multipleComp.snakefile")
         if rMats:
             include: os.path.join(maindir, "shared", "rules", "rMats.multipleComp.snakefile")
@@ -146,27 +158,39 @@ def run_Trimming(trim, fastqc):
 
 def run_alignment_free():
     if "alignment-free" in mode:
-        file_list = [
-        expand("Salmon/{sample}.quant.sf", sample=samples),
-        "Salmon/TPM.transcripts.tsv",
-        "Salmon/counts.transcripts.tsv",
-        expand("Salmon/{sample}/abundance.h5", sample=samples) ]
-
-        if sampleSheet:
-            sample_name = os.path.splitext(os.path.basename(sampleSheet))[0]
-            if not isMultipleComparison:
-                file_list.append( ["DESeq2_Salmon_{}/DESeq2.session_info.txt".format(sample_name)])
-                if cf.check_replicates(sampleSheet):
-                    file_list.append( ["sleuth_Salmon_{}/so.rds".format(sample_name)] )
-                if rMats:
-                    file_list.append( ["rMats_{}/RI.MATS.JCEC.txt".format(sample_name)] )
-                    file_list.append( ["rMats_{}/b2.csv".format(sample_name)] )
-            else:
-                file_list.append(expand("DESeq2_Salmon_{}".format(sample_name) + ".{compGroup}/DESeq2.session_info.txt",compGroup=cf.returnComparisonGroups(sampleSheet)))
-                file_list.append(expand("sleuth_Salmon_{}".format(sample_name) + ".{compGroup}/so.rds",compGroup=cf.returnComparisonGroups(sampleSheet)))
-                if rMats:
-                    file_list.append(expand("rMats_{}".format(sample_name) + ".{compGroup}/RI.MATS.JCEC.txt",compGroup=cf.returnComparisonGroups(sampleSheet)))
-                    file_list.append(expand("rMats_{}".format(sample_name) + ".{compGroup}/b2.csv",compGroup=cf.returnComparisonGroups(sampleSheet)))
+        if not "allelic-mapping" in mode:
+            file_list = [
+            expand("Salmon/{sample}.quant.sf", sample=samples),
+            "Salmon/TPM.transcripts.tsv",
+            "Salmon/counts.transcripts.tsv",
+            expand("Salmon/{sample}/abundance.h5", sample=samples) ]
+
+            if sampleSheet:
+                sample_name = os.path.splitext(os.path.basename(sampleSheet))[0]
+                if not isMultipleComparison:
+                    file_list.append( ["DESeq2_Salmon_{}/DESeq2.session_info.txt".format(sample_name)])
+                    if cf.check_replicates(sampleSheet):
+                        file_list.append( ["sleuth_Salmon_{}/so.rds".format(sample_name)] )
+                    if rMats:
+                        file_list.append( ["rMats_{}/RI.MATS.JCEC.txt".format(sample_name)] )
+                        file_list.append( ["rMats_{}/b2.csv".format(sample_name)] )
+                else:
+                    file_list.append(expand("DESeq2_Salmon_{}".format(sample_name) + ".{compGroup}/DESeq2.session_info.txt",compGroup=cf.returnComparisonGroups(sampleSheet)))
+                    file_list.append(expand("sleuth_Salmon_{}".format(sample_name) + ".{compGroup}/so.rds",compGroup=cf.returnComparisonGroups(sampleSheet)))
+                    if rMats:
+                        file_list.append(expand("rMats_{}".format(sample_name) + ".{compGroup}/RI.MATS.JCEC.txt",compGroup=cf.returnComparisonGroups(sampleSheet)))
+                        file_list.append(expand("rMats_{}".format(sample_name) + ".{compGroup}/b2.csv",compGroup=cf.returnComparisonGroups(sampleSheet)))
+        else:
+            file_list = [
+            expand("SalmonAllelic/{sample}.{allelic_suffix}.quant.sf", sample=samples,allelic_suffix=allelic_suffix),
+            "SalmonAllelic/TPM.transcripts.tsv",
+            "SalmonAllelic/counts.transcripts.tsv",
+            expand("SalmonAllelic/{sample}.{allelic_suffix}/abundance.h5", sample=samples,allelic_suffix=allelic_suffix) ]
+            if sampleSheet:
+                sample_name = os.path.splitext(os.path.basename(sampleSheet))[0]
+                if not isMultipleComparison:
+                    file_list.append( ["DESeq2_SalmonAllelic_{}/DESeq2.session_info.txt".format(sample_name)])
+                    file_list.append( ["sleuth_SalmonAllelic_{}/so.rds".format(sample_name)] )
         return(file_list)
     else:
         return([])
@@ -309,8 +333,6 @@ onstart:
 ################################################################################
 
 if not fromBAM:
-    localrules: Salmon_wasabi, sleuth_Salmon
-
 
     rule all:
         input:
@@ -325,11 +347,11 @@ if not fromBAM:
             "multiQC/multiqc_report.html"
 
 else:
-    localrules: Salmon_wasabi
 
     rule all:
         input:
             run_alignment(),
+            run_allelesp_mapping(),
             run_deepTools_qc(),
             run_GenomicContamination(),
             "multiQC/multiqc_report.html"
diff --git a/snakePipes/workflows/mRNA-seq/cluster.yaml b/snakePipes/workflows/mRNA-seq/cluster.yaml
index bff08a4e8..9b340f000 100644
--- a/snakePipes/workflows/mRNA-seq/cluster.yaml
+++ b/snakePipes/workflows/mRNA-seq/cluster.yaml
@@ -14,9 +14,13 @@ annotation_bed2fasta:
     memory: 4G
 sleuth_Salmon:
     memory: 4G
+sleuth_SalmonAllelic:
+    memory: 10G
 DESeq2:
     memory: 5G
-DESeq2_Salmon:
+DESeq2_Salmon_basic:
+    memory: 3G
+DESeq2_Salmon_allelic:
     memory: 3G
 star_index:
     memory: 15G
diff --git a/snakePipes/workflows/mRNA-seq/mRNA-seq b/snakePipes/workflows/mRNA-seq/mRNA-seq
index d3cb61b46..2a62d8bd4 100755
--- a/snakePipes/workflows/mRNA-seq/mRNA-seq
+++ b/snakePipes/workflows/mRNA-seq/mRNA-seq
@@ -152,8 +152,8 @@ def main():
             sys.exit("{} is not a valid mode!\n".format(mode))
     if "alignment" not in modeTemp and args.UMIDedup:
         sys.exit("UMIDedup is only valid for \"alignment\" mode!\n")
-    if args.fromBAM and ("alignment-free" in modeTemp or "allelic-mapping" in modeTemp):
-        sys.exit("\n--fromBAM can only be used with modes \'alignment\' or \'deepTools_qc\' - use one of these modes or provide fastq files!\n")
+    if args.fromBAM and ("alignment-free" in modeTemp ):
+        sys.exit("\n--fromBAM can only be used with modes \'alignment\' , \'allelic-mapping\'  or \'deepTools_qc\' - use one of these modes or provide fastq files!\n")
     if args.fromBAM:
         args.aligner = "EXTERNAL_BAM"
     if args.rMats and not args.sampleSheet: