GMAP or Bowtie index from FASTA of genes

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5.9 years ago

gtasource ▴ 60

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!

GMAP bowtie • 2.1k views

ADD COMMENT • link updated 5.8 years ago by Biostar 20 • written 5.9 years ago by gtasource ▴ 60

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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 REPLY • link 5.9 years ago by WouterDeCoster 47k

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I keep getting errors

And what are the errors?

ADD REPLY • link 5.9 years ago by h.mon 35k

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