Bowtie Building Index Issue

Question

[Arpssss]

I am trying to use BowTie for short read alignment on human genome. Now, after installing it I run the command of it's examples and find it is working nicely. However, actually I want to build index of full human genome data using BowTie. But, can't understand how to do that means which commands I have to run in-order to build BowTie index on that data. And also which command I have to run in-order to find match (outputted on a file) on query file. Can anybody kindly help me by providing pointer or commands to do that. I go through their manual, however can not found any suitable example. Thanks in advance.

[Ryan Thompson]

All your questions are answered in the Bowtie2 manual. See here for usage of the bowtie2 command, and here for the bowtie2-build command. You also seem confused because you are referring to Bowtie 2 as just "Bowtie", but they are different programs and not compatible with each other. Based on your question, people might give you answers for Bowtie that would be wrong for Bowtie 2.

Answer 1

[Istvan Albert]

What you need is to combine the files from the file named chromFa.tar.gz into a single one

cat *.fa > hg19.fa

then run the command as described in the manual:

bowtie2-build hg19.fa hg19

Better yet download the indices directly from http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

[Arpssss]

Thanks a lot. If I want to use hg19.2bit, can I just transform .2bit to .fa and use that bowtie command ?

[Arpssss]

Another point is that how to run query read file and take output in a file ?

[zhidong.yuan]

Of course, you can do that.

[gavriellakaplan]

i ran the following: cat *.fa > hg19_chr1.fa bowtie2-build hg19_chr1.fa

And after it ran a traceback I received: OSError: [Errno 8] Exec format error

Please advise.

[mariakondili13]

late but for the record: You have two commands in one line that have no logic continuation : 1. cat *.fa > hg19_chr1.fa 2. bowtie2-build hg19_chr1.fa hg19 Maybe it would work if you do pipe of 1st on 2nd :

cat *.fa > hg19_chr1.fa | bowtie2-build hg19