How to get fasta sequences based on bt2 index?

Question

[biolab]

Dear all,

I have a simple question: Is it possible to get the genome sequences based on the six bt2 index files created by bowtie2? How to achieve this?

Actually I am writing a simple bash pipeline to conduct RNAseq analysis. TOPHAT2 requires genome INDEX, but does not need genome.fa as input. In contrast, CUFFDIFF has a parameter (-b) for genome.fa, without requiring genome INDEX. So I just want INDEX as input. Thank you very much!

Answer 1

[G.S]

Hello,

In order to get the sequences from which the bt2 index files came from you can use bowtie2-inspect as follows:

bowtie2-inspect <bt2_base>

If you run the command above with your bt2 index files, the tool will output a FASTA file containing the sequences of the original references.

There are also some options available, you can check the bowtie2 manual.

Cheers!

[Matt Shirley]

I never knew about this. Thanks for pointing it out. Do you know if there's something similar for bwa?

[biolab]

Thank you G.S, your answer is very helpful!

[G.S]

As far as I know, there isn't something similar for BWA, but I'm not sure about it !