Question: How do I setup the pre-built indexed reference for Bowtie2
gravatar for field654
11 days ago by
field6540 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 • 88 views
ADD COMMENTlink modified 10 days ago • written 11 days ago by field6540

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 11 days ago by karl.stamm3.7k

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 11 days ago by field6540

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 11 days ago by genomax87k

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 11 days ago by field6540
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