How to use GSNAP/GMAP for mm10 genome

Question

[Moneeb Bajwa]

Hello,

I am not sure how to download the mm10 genome for genome guided alignment on GSNAP. In a separate project (for an Aiptasia alignment), I used an .fna file for building the gmap database and a .gff file for the intron store building, and I used Trinity subsequently (these files were provided for me and I didn't download them so I don't know where to get them). I wish to follow this protocol for my mm10 alignment for my mouse sequences if possible.

I appreciate your help!

Answer 1

[GenoMax]

This is the GENCODE official data page for all things related to mouse genome. You will find the files you need there (fasta genome sequence, GTF annotation).

[Moneeb Bajwa]

Thank you. Does it matter which combination I choose? Could I choose the first in the gff list with the first in the fasta file list? I also see that it is .fa as opposed to .fna; does that matter?

[GenoMax]

.fa should be equivalent to .fna. Please read the descriptions for the files carefully before selecting. If you are not interested in patches and haplotypes then choose the files labelled as PRI (Primary) only.

[Moneeb Bajwa]

Also what if I did not unzip the files when supplying them to GSNAP and the other tools; would it work?

[GenoMax]

It would depend on the tool. Some tools can accept gzipped files others you will need to unzip them.