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Chip-Seq analysis in Biostar handbook

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
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written by s_bio • s_bio

2 answers

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

Best,

Agata

• 0 views • link
written by agata88 agata88

Thanks for your reply agata :-)

will try building the index

• 0 views • link
written by s_bio • s_bio

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