Question: How to use GSNAP/GMAP for mm10 genome
0
gravatar for Moneeb Bajwa
4 months ago by
Delaware, USA
Moneeb Bajwa0 wrote:

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!

ADD COMMENTlink modified 4 months ago by genomax59k • written 4 months ago by Moneeb Bajwa0
2
gravatar for genomax
4 months ago by
genomax59k
United States
genomax59k wrote:

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).

ADD COMMENTlink modified 4 months ago • written 4 months ago by genomax59k

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?

ADD REPLYlink modified 4 months ago • written 4 months ago by Moneeb Bajwa0
1

.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.

ADD REPLYlink written 4 months ago by genomax59k

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

ADD REPLYlink written 4 months ago by Moneeb Bajwa0
1

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

ADD REPLYlink written 4 months ago by genomax59k
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