Download and process SRA data

1. Download SRA data

#BSUB -J blast
#BSUB -n 10
#BSUB -R span[hosts=1]
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -q normal
cd /public/home/qtxu/Data/Chip_seq_data/DNA_acetylation/Arabidopsis 

prefetch SRR13912624     -O ./

2. Coverte sra data to fq data

fastq-dump --split-3  --gzip   ../SRR14780693/met1.sra  # --split-3 is for paired end data

3. Clean fq data

fastp -i  met1_1.fastq.gz   -I  met1_2.fastq.gz    -o met1_4ac_R1.fq.gz  -O met1_4ac_R2.fq.gz
#-i and -I are input data

4. Map data and call peaks

#BSUB -J blast
#BSUB -n 10
#BSUB -R span[hosts=1]
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -q normal

cd /public/home/qtxu/Data/Chip_seq_data/DNA_acetylation/Arabidopsis 

bowtie2 -x  ../../Ref/Arabidopsis  -1  met1_4ac_R1.fq.gz     -2   met1_4ac_R2.fq.gz    -S WT_1.sam  2> algn_log

samtools view  -bS WT_1.sam  > WT_1.bam

samtools sort -l 9 -o  WT_1_sorted.bam  -O BAM   WT_1.bam

 samtools view -bF 12  WT_1_sorted.bam   >  WT_1_mapped.bam

samtools   rmdup -S   WT_1_mapped.bam  met1_rmp.bam

samtools  index    met1_rmp.bam

macs2 callpeak -t   met1_rmp.bam  -f BAMPE -B -q 0.05 -g 3.6e+8 -n met1