Chip-Seq analysis in Biostar handbook

Question

[s_bio]

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

Answer 1

[agata88]

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

Best,

Agata

Answer 2

[s_bio]

Thanks for your reply agata :-)

will try building the index