Question: Chip-Seq analysis in Biostar handbook
0
gravatar for s_bio
3.4 years ago by
s_bio10
s_bio10 wrote:

Hi All,

I am trying to follow chip-seq analysis pipeline from biostar handbook. I am trying to follow Ming Tangs guide for the same. However, in the handbook it is recommended to load Bowtie2 aligner which I did. Now, I am facing problem in following command in how to align chip-seq reads section.

bowtie -p 10 --best --chunkmbs 320 /risapps/reference/bowtie1/hg19 -q YAP1.fastq -S ../results/bams/YAP1.sam

however I modified the command as follows:

bowtie -p 10 --best --chunkmbs 320 /src/bowtie2-2.2.9/hg19 -q YAP1.fastq -S ../results/bams/YAP1.sam

but I got this error Could not locate a Bowtie index corresponding to basename "/src/bowtie2-2.2.9/hg19"

I want to know is my modification correct and How to solve this error?????????

Thanks

chip-seq • 1.1k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by s_bio10
3
gravatar for agata88
3.4 years ago by
agata88800
Poland
agata88800 wrote:

i think bowtie needs indexed reference. Try bowtie-build to your hg19 reference,

Best,

Agata

ADD COMMENTlink written 3.4 years ago by agata88800
0
gravatar for s_bio
3.4 years ago by
s_bio10
s_bio10 wrote:

Thanks for your reply agata :-)

will try building the index

ADD COMMENTlink written 3.4 years ago by s_bio10
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