1. #!/bin/bash
    3. analysis_dir=$1
    4. config_file=$2
    5. number1=$3
    6. number2=$4
    7. conda activate chip
    8. mkdir -p {raw,clean,align,peaks,motif,qc,log}
    9. index=/home/yb77613/reference/index/bowtie/hg38
    10. # for config.txt
    11. # sampleName and fastq files(for single end)
    12. # input /home/vip28/data/public/wen_chipseq/raw/SRR3356385.fastq.gz
    13. # MYCN  /home/vip28/data/public/wen_chipseq/raw/SRR3356386.fastq.gz
    14. # TWIST /home/vip28/data/public/wen_chipseq/raw/SRR3356388.fastq.gz
    15. cat $config_file |while read id
    16. do
    17. echo $id
    18.     arr=($id)
    19.     fq=${arr[1]}
    20.     sample=${arr[0]}
    21.     if((i%$number1==$number2))
    22.     then
    23.     ## step1: basic QC for fastq files
    24.     if [  ! -f  ok.fastp.$sample.status ]; then
    25.           fastp -i $fq -o clean/${sample}.fq.gz \
    26.           --thread=4 --length_required=36 --n_base_limit=6 \
    27.           --compression=6 -R ${sample}  \
    28.           1>log/log.fastp.${sample}.txt 2>&1
    29.     fi ## end for if files
    30.     if [ $? -eq 0 ]; then
    31.              touch  ok.fastp.$sample.status
    32.                 else
    33.                      echo "fastp failed" $sample
    34.     fi
    35.     fastqc $fq  -O qc
    36.     fastqc clean/${sample}.fq.gz -O qc
    37.     ## step2: alignment
    38.     if [  ! -f  ok.bowtie2.$sample.status ]; then
    39.           bowtie2  -p 4  -x  $index -U  clean/${sample}.fq.gz  | \
    40.           samtools sort  -O bam  -@ 4 -o - > align/${sample}.bam
    41.     fi ## end for if files
    42.     if [ $? -eq 0 ]; then
    43.              touch  ok.bowtie2.$sample.status
    44.           else
    45.              echo "bowtie2 failed" $sample
    46.     fi
    49.     ## step3: QC for bam files
    50.     if [  ! -f  ok.sambamba.$sample.status ]; then
    51.            sambamba markdup  -r  align/${sample}.bam align/${sample}_rmd.bam
    52.     fi ## end for if files
    53.     if [ $? -eq 0 ]; then
    54.              touch  ok.sambamba.$sample.status
    55.           else
    56.              echo "sambamba failed" $sample
    57.     fi
    58.     samtools flagstat  align/${sample}.bam   >  qc/${sample}.flagstat
    59.     samtools flagstat  align/${sample}_rmd.bam   >  qc/${sample}_rmd.flagstat
    61.     ## step4: call peaks
    62.     if [  ! -f  ok.macs2.$sample.status ]; then
    63.         macs2 callpeak -t align/${sample}_rmd.bam -f BAM -g hs -n ${sample}_rmd -B -q 0.01 --outdir  peaks
    64.         macs2 callpeak -t align/${sample}.bam -f BAM -g hs -n ${sample}_raw -B -q 0.01 --outdir  peaks
    65.     fi ## end for if files
    66.     if [ $? -eq 0 ]; then
    67.              touch  ok.macs2.$sample.status
    68.           else
    69.              echo "macs2 failed" $sample
    70.     fi
    74.     fi # check the number1 number2
    75.     i=$((i+1))
    76. done