This pipeline is based on ATAC-seq tutorial:

• file name: template_fqc.sh
• commande: fastqc -o ../results/_fastqc2/ --dir ../results/_TMP -f fastq $f1

• file name: template_mqc.sh
• commande: multiqc --outdir ../results/_fastqc ../results/_fastqc

• file name: template_trimmomatic.sh
• options:
• ILLUMINACLIP:sequencing-adapters.fa:2:30:5
• SLIDINGWINDOW:5:20
• HEADCROP:10
• MINLEN:16
• commande: java -jar -Xmx8g $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar PE -threads 40 -trimlog $logfile $f1 $f2 $fwP $fwU $rvP $rvU ILLUMINACLIP:sequencing-adapters.fa:2:30:5 SLIDINGWINDOW:5:20 HEADCROP:10 MINLEN:16
• FastQC commandes:
  • fastqc -o ../results/_fastqc2/ --dir ../results/_TMP -f fastq $fwP
  • fastqc -o ../results/_fastqc2/ --dir ../results/_TMP -f fastq $rvP

• file name: template_mqc1.sh
• commande: multiqc --outdir ../results/_fastqc2 ../results/_fastqc2

• file name: template_bowtie2.sh
• options:
• --very-sensitive
• -X 1000
• -k 10
• commande:
bowtie2 --threads 40 --very-sensitive -X 1000  -k 10 --un $ump --al $mmp  --met-file $metric $rgline -x $indx -1 $f1 -2 $f2 -S $sam 2>$logf

• file name: template_samstat1.sh
• commande: samtools stats $sam >$samstat

• file name: template_mqc2.sh
• commande: mugqic/MultiQC/1.14 -m bowtie2 --outdir ../results/_logs/_bowtie2 $WORK_DIR/$1/results/_logs/_bowtie2/*

• commande: samtools sort -@ 48 -o $ssam $sam

• file name: template_bFilter_sam.sh
• commandes:
• samtools index $f1 # to filter by chromosome, samtools need indexed bam input
• samtools view -H $f1 | grep -v "@SQ\sSN:GU592207\.1\sLN:134551" >$filtered
• loup over wanted chromosomes:
mapfile -t lines < $chroms
for line in "${lines[@]}"; do samtools view $f1 $line >>$filtered; done

• commande: samtools view -Sb $filtered > $bam

• file name: template_mqc3.sh
• commande: mugqic/MultiQC/1.14 -m samtools --outdir ../results/_BAM/_filtered $WORK_DIR/$1/results/_BAM/_filtered/*_filtered_stats.txt

• file name: template_sambambaMarkDup.sh
• commande: sambamba markdup $f1 $marked

• file name: template_bam2bed.sh
• command: bedtools bamtobed -color 255,0,0 -bed12 -cigar -i $f1 > $bed

• file name: template_macs2.sh
• commande: macs2 callpeak -t $f1 --nomodel -g 379627553 -f BED -n $out -q 0.05 --extsize 200 --shift -100 --keep-dup all -B