diff --git a/dRep-pipeline.md b/dRep-pipeline.md index 40b8549..71df1ef 100644 --- a/dRep-pipeline.md +++ b/dRep-pipeline.md @@ -10,15 +10,10 @@ [TPM-normalization](#TPM-normalization) [Basic-statistics](#Basic-statistics) -# Description - -![iMGMC-pipeline](/images/pipeline.png) - # Requirements * [BBmap](https://sourceforge.net/projects/bbmap/) * [samtools](http://samtools.sourceforge.net/) * [sambamba](http://lomereiter.github.io/sambamba/) -* iMGMC repository # Data-pre-processing @@ -55,10 +50,10 @@ You can use bbmap and the reference pig genome from and assign the ${PIGgenome} wget -O PIBAC-mMAGs.tar.gz "https://onedrive.live.com/" -**2. Index iMGMC catalog** +**2. Index PIBAC catalog** - tar -xzf iMGMC-hqMAGs-dereplicated_genomes.tar.gz - bbsplit.sh ref=iMGMC-hqMAGs-dereplicated_genomes + tar -xzf PIBAC-hqMAGs-dereplicated_genomes.tar.gz + bbsplit.sh ref=PIBAC-hqMAGs-dereplicated_genomes # Mapping @@ -74,16 +69,3 @@ For this tutorial we use bbmap for mapping the reads to MAG collection. You can sortscafs=f nzo=f \ in=${SampleName}_R1_rmhost.fastq.gz \ in2=${SampleName}_R2_rmhost.fastq.gz - - -# TPM-normalization -You need to normalize you samples counts for a comparison. Here we use TPM-normalization to create TPM-${SampleID}.txt form ${SampleName}.covstat : - - makeTPMfromCovStats.sh ${SampleName}.covstat - - -# Basic-statistics - -under construction - -