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?????????