bowtie2 indices from separate chromosome fasta files

[alyamahmoud]

Hi

I have separate fasta files for each chromosome of the cow genome. I need to build bowtie2 indices for later tophat alignment. What's the best way to go from here:
Do I cat all fasta files into one fast file or do I just run bowtie build on the separate fasta files ?

Thanks a lot
Alyaa

[GenoMax]

"cat" all fasta files into a single "genome" file and build indexes from the single file. You will need access to a machine that has enough RAM.

If you can use indexes provided by illumina (fasta sequence, bwa/bowtie indexes, annotations) then you can get the pre-formatted sequences/indexes from the iGenomes page: http://support.illumina.com/sequenci...e/igenome.ilmn

[alyamahmoud]

Good thanks a lot

I am afraid the iGenome package provide preformated indices for specific genomes only, true ?

[dpryan]

Yeah, and Bos taurus is one of them (not that its difficult to index things yourself).

[Sabine_Holz]

It is also possible to do the following:

type several fasta-files like fasta1.fa,fasta2.fa,fasta3.fa

just "," in between works fine, during the index building all fasta files are named as input and the building of an index works good