Question: How do I setup the pre-built indexed reference for Bowtie2
gravatar for field654
5 months ago by
field65410 wrote:


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 ""

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.


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

assembly • 294 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by field65410

Do you have a genome file? What's it look like? Bowtie should have a creator script for indexing a genome file.

ADD REPLYlink written 5 months ago by karl.stamm3.9k

Yes it does. It's bowtie2-build "genome" "export basename for reference".

I'm really new to bioinformatics and bowtie2. I should definitely have tried that.

I started with the pre-built reference though.

Thank you for you kind help.

ADD REPLYlink written 5 months ago by field65410

You will need to add basename for the index after the directory name. If you downloaded pre-built indexes from Bowtie site they should be fine to use as is.

ADD REPLYlink written 5 months ago by GenoMax95k

As a matter of fact, when I entered the folder of the index and inspected it worked. I assume the previous time I failed because I mistyped the file name where I missed a "_" or so.

Thank you so much.

ADD REPLYlink written 5 months ago by field65410
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