Hi,

This is really basic but how to I set up the prebuilt reference?

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

I got the reference from the above link. The reference I tried is named "grch38_1kgmaj_bt2.zip"

After I unzipped I got 6 files, with the same base name and suffixes of .1 .2 .3 .4 .rev.1 .rev.2

That's exactly like the described, built reference. So I copied them to a new folder /BOWTIE2-INDEXES/grch38_1kgmaj_bt2

But when I tried either the align with the reference or inspect, the bowtie2 program won't recognize the folder as a reference.

Like I used the command within the dir to where I copied the 6 files:

bowtie2-inspect grch38_1kgmaj

I simply got the error

Could not locate a Bowtie index corresponding to basename "grch_38_1kgmaj"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-inspect-s --wrapper basic-0 grch_38_1kgmaj

It seems that I have to tell the program somehow that I had the reference here.

Thank you.

Field

Problem solved. It didn't work for me either because I mistyped the file name or I didn't type the base name after the directory