Question: GMAP or Bowtie index from FASTA of genes
0
gravatar for gtasource
7 months ago by
gtasource20
gtasource20 wrote:

Hi all,

I'm looking to use either Bowtie2 or GMAP/GSNAP to try to map sequences to gene names. The FASTA file that I want to index contains all of the genes from a species. Problem is, I keep getting errors when I try to index this FASTA file, as GMAP wants a chromosomal assembly I believe. The problem with using the chromosome assembly as an index, is it won't tell me what that gene is (hence why I create my own FASTA with gene names.) Does anybody have any suggestions for this?

Cheers!

bowtie gmap • 347 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 7 months ago by gtasource20
1

You should align to the genome, and GMAP is perfectly capable of doing so. It is however unclear which sequences you are trying to map. If you have all genes from a species you most likely could also get a GTF/GFF annotation file from this species, which would tell you which gene is where on the genomic DNA.

For now it is unclear which problem you are trying to solve.

ADD REPLYlink written 7 months ago by WouterDeCoster40k
1

I keep getting errors

And what are the errors?

ADD REPLYlink written 7 months ago by h.mon26k
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