教你学会ChIP-seq分析 | 第五讲

## step5 : alignment to hg19/ using bowtie2 to do alignment

## ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2-build ~/biosoft/bowtie/hg19_index /hg19.fa ~/biosoft/bowtie/hg19_index/hg19

## cat >run_bowtie2.sh

ls *.fastq | while read id ;

do

echo $id

#~/biosoft/bowtie/bowtie2-2.2.9/bowtie2 -p 8 -x ~/biosoft/bowtie/hg19_index/hg19 -U $id -S ${id%%.*}.sam 2>${id%%.*}.align.log;

#samtools view -bhS -q 30 ${id%%.*}.sam > ${id%%.*}.bam ## -F 1548 https://broadinstitute.github.io/picard/explain-flags.html

# -F 0x4 remove the reads that didn't match

samtools sort $ {id%%.*}.bam ${id%%.*}.sort ## prefix for the output

# samtools view -bhS a.sam | samtools sort -o - ./ > a.bam

samtools index $ {id%%.*}.sorted.bam

done

SRR1042593 .fastq

16902907 reads; of these:

16902907 ( 100.00 %) were unpaired; of these:

667998 ( 3.95 %) aligned 0 times

12467095 ( 73.76 %) aligned exactly 1 time

3767814 ( 22.29 %) aligned > 1 times

96.05 % overall alignment rate

......

SRR1042598 .fastq

58068816 reads; of these:

58068816 ( 100.00 %) were unpaired; of these:

8433671 ( 14.52 %) aligned 0 times

37527468 ( 64.63 %) aligned exactly 1 time

12107677 ( 20.85 %) aligned > 1 times

85.48 % overall alignment rate

[ samopen] SAM header is present: 93 sequences.

SRR1042599 .fastq

24019489 reads; of these:

24019489 ( 100.00 %) were unpaired; of these:

1411095 ( 5.87 %) aligned 0 times

17528479 ( 72.98 %) aligned exactly 1 time

5079915 ( 21.15 %) aligned > 1 times

94.13 % overall alignment rate

[ samopen] SAM header is present: 93 sequences.

SRR1042600 .fastq

76361026 reads; of these:

76361026 ( 100.00 %) were unpaired; of these:

8442054 ( 11.06 %) aligned 0 times

50918615 ( 66.68 %) aligned exactly 1 time

17000357 ( 22.26 %) aligned > 1 times

88.94 % overall alignment rate

[ samopen] SAM header is present: 93 sequences.