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