05

自学CHIP-seq分析第五讲~测序数据比对

## 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 (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
[samopen] SAM header is present: 93 sequences.
SRR1042594.fastq
60609833 (100.00%) were unpaired; of these:
9165487 (15.12%) aligned 0 times
39360173 (64.94%) aligned exactly 1 time
12084173 (19.94%) aligned >1 times
84.88% overall alignment rate
[samopen] SAM header is present: 93 sequences.
SRR1042595.fastq
14603295 (100.00%) were unpaired; of these:
918028 (6.29%) aligned 0 times
10403045 (71.24%) aligned exactly 1 time
3282222 (22.48%) aligned >1 times
93.71% overall alignment rate
[samopen] SAM header is present: 93 sequences.
SRR1042596.fastq
65911151 (100.00%) were unpaired; of these:
10561790 (16.02%) aligned 0 times
42271498 (64.13%) aligned exactly 1 time
13077863 (19.84%) aligned >1 times
83.98% overall alignment rate
[samopen] SAM header is present: 93 sequences.
SRR1042597.fastq
22210858 (100.00%) were unpaired; of these:
1779568 (8.01%) aligned 0 times
15815218 (71.20%) aligned exactly 1 time
4616072 (20.78%) aligned >1 times
91.99% overall alignment rate
[samopen] SAM header is present: 93 sequences.
SRR1042598.fastq
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 (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 (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.