Hi All,

I am trying to align my paired-end ChIP seq data to the Arabidopsis genome (TAIR10), but am not able to do so with Bowtie2 because it keeps saying it "does not exist or is not a Bowtie 2 index"

I downloaded the file from the bowtie website and the folder has the six .bt2 files as expected.

The code I am trying is:

bowtie2 -p 4 -x .../Desktop/merged_retrims/TAIR10/tair10 -1 Col-Mock-1-IgG_R1.fq.gz -2 Col-Mock-1-IgG_R1.fq.gz > Col-Mock-1-H2Bub1.sam

All of my files are in the merged_retrims directory. I installed bowtie2 using conda. Any advice or pointers is very appreciated.