reorganizing

.gitignore

@@ -0,0 +1,9 @@
+working/*
+.env
+.DS_Store
+*/.env
+*/.DS_Store
+metadata/database.conf
+metadata/*.sif
+metadata/run/
+metadata/var-lib-rstudio-server/

scripts/0_rrbs_mkdir.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+mkdir /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments
+mkdir /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs
+mkdir /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC
+mkdir /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC/fastqc
+mkdir /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC/qualimap
+

scripts/10_samtools.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -N 1 
+#SBATCH -n 8 
+#SBATCH -J samtools
+#SBATCH --mem=8GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/samtools-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/samtools-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${align_dir}/*_trimmomatic_bismark_bt2.bam))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic_bismark_bt2.bam)
+
+samtools sort -o ${align_dir}/${bn}_trimmomatic_bismark_bt2.sorted.bam ${align_dir}/${bn}_trimmomatic_bismark_bt2.bam 

scripts/11_qualimap.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -N 1 
+#SBATCH -n 8 
+#SBATCH -J qualimap
+#SBATCH --mem=8GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/qualimap-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/qualimap-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${align_dir}/*_trimmomatic_bismark_bt2.sorted.bam)) 
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic_bismark_bt2.sorted.bam)
+
+qualimap bamqc -bam ${align_dir}/${bn}_trimmomatic_bismark_bt2.sorted.bam -outdir ${qc_dir}/qualimap
+

scripts/2_rrbs_fastqc.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH -t 12:00:00
+#SBATCH -n 8
+#SBATCH -N 1
+#SBATCH -J rrbs_fastqc
+#SBATCH --mem=16GB
+#SBATCH --mail-type=ALL
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_fastqc-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_fastqc-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${fastq_dir}/*_R1_001.fastq.gz))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _R1_001.fastq.gz)
+
+fastqc -o ${qc_dir}/fastqc ${fastq_dir}/${bn}_R1_001.fastq.gz

scripts/3_rrbs_trim_galore.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -n 8
+#SBATCH -N 1
+#SBATCH -J trim_galore
+#SBATCH --mem=32GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_trimgalore-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_trimgalore-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${fastq_dir}/*fastq.gz))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} .fastq.gz)
+
+trim_galore --quality 20 --clip_R1 6 --adapter AGATCGGAAGAGC --output_dir ${fastq_dir} --basename "${bn}_trimgalore" --rrbs ${fastq_dir}/${bn}.fastq.gz
+
+echo ${bn}
+

scripts/4_rrbs_trimmomatic.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -t 48:00:00
+#SBATCH -n 8
+#SBATCH -N 1
+#SBATCH -J trimmomatic
+#SBATCH --mem=32GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_trimmomatic-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_trimmomatic-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${fastq_dir}/*_trimgalore_trimmed.fq.gz))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimgalore_trimmed.fq.gz)
+
+trimmomatic SE -threads 8 -trimlog ${log_dir}/${bn}_trimmomatic.log ${fastq_dir}/${bn}_trimgalore_trimmed.fq.gz ${fastq_dir}/${bn}_trimmomatic.fastq.gz ILLUMINACLIP:/gpfs/data/cbc/cbc_conda_v1/envs/cbc_conda/opt/trimmomatic-0.36/adapters/TruSeq3-SE.fa:2:30:5:6:true SLIDINGWINDOW:4:20 MINLEN:35
+

scripts/5_rrbs_fastqc_trimmed.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -n 8
+#SBATCH -N 1
+#SBATCH -J fastqc_trimmed
+#SBATCH --mem=32GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_fastqc_trimmed-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_fastqc_trimmed-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${fastq_dir}/*_trimmomatic.fastq.gz))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic.fastq.gz)
+
+fastqc -o ${qc_dir}/fastqc ${fastq_dir}/${bn}_trimmomatic.fastq.gz

scripts/6_rrbs_align.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -n 16
+#SBATCH -N 1
+#SBATCH -J rrbs_align
+#SBATCH --mem=160GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_align-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/rrbs_align-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${fastq_dir}/*_trimmomatic.fastq.gz))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic.fastq.gz)
+
+bismark -o ${align_dir} --bowtie2 --genome /gpfs/data/shared/databases/refchef_refs/S_scrofa/primary/bismark_index --un --pbat ${fastq_dir}/${bn}_trimmomatic.fastq.gz

scripts/7_bismark_report.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -n 1
+#SBATCH -N 1
+#SBATCH -J bismark_summary
+#SBATCH --mem=8GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/bismark_summary-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/bismark_summary-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${align_dir}/*_trimmomatic_bismark_bt2_SE_report.txt))
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic_bismark_bt2_SE_report.txt)
+
+bismark2report --alignment_report ${align_dir}/${bn}_trimmomatic_bismark_bt2_SE_report.txt --dir ${qc_dir}

scripts/8_bismark_extract.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -N 1 
+#SBATCH -n 8 
+#SBATCH -J bismark_extractor
+#SBATCH --mem=8GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/bismark_extractor-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/bismark_extractor-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${align_dir}/*_trimmomatic_bismark_bt2.bam)) 
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic_bismark_bt2.bam)
+
+bismark_methylation_extractor --bedGraph --comprehensive --ignore_3prime 6 -s --merge_non_CpG --report --output ${qc_dir} --gzip --multicore 8 --genome_folder /gpfs/data/shared/databases/refchef_refs/S_scrofa/primary/bismark_index/ ${align_dir}/${bn}_trimmomatic_bismark_bt2.bam 

scripts/9_bismark_bam2nuc.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -t 24:00:00
+#SBATCH -N 1 
+#SBATCH -n 8 
+#SBATCH -J bam2nuc
+#SBATCH --mem=8GB
+#SBATCH --array=1-18
+#SBATCH -e /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/bam2nuc-%A-%a-%J.err
+#SBATCH -o /gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs/bam2nuc-%A-%a-%J.out
+
+source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
+conda activate fedulov_rrbs
+
+fastq_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Sequencing_Files"
+align_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Alignments"
+log_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/Logs"
+qc_dir="/gpfs/data/cbc/fedulov_alexey/Fedulov_porcine_rrbs/working/QC"
+
+input=($(ls ${align_dir}/*_trimmomatic_bismark_bt2.bam)) 
+bn=$(basename ${input[$((SLURM_ARRAY_TASK_ID -1))]} _trimmomatic_bismark_bt2.bam)
+
+bam2nuc --dir ${qc_dir} --genome_folder /gpfs/data/shared/databases/refchef_refs/S_scrofa/primary/bismark_index/ ${align_dir}/${bn}_trimmomatic_bismark_bt2.bam