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2 hours ago by

Hi all,

I am doing an assembly of a non-model organism transcriptome. I assembled the RNA-seq reads with Trinity (genome-guided assembly) and to get the gff, I mapped the fasta output from Trinity to the reference genome using GMAP. The gff output has MANY instances where even if the direction is specified as 'sense', the sign in the direction column is '-'. Same happens when the direction is 'antisense'. I thought it was weird because that seems to happen pretty much exactly half of the times. Here is an example:

LQNS02276481.1 phaw gene 17436406 17487190 . + . ID=TRINITY_GG_63141_c0_g1_i1.path1;Name=TRINITY_GG_63141_c0_g1_i1;Dir=antisense

I checked, and the correct direction seems to always be in 'Dir=', not in the direction column (the 7th column here, '+')

The command I ran was:
gmap -d phaw --gff3-add-separators=0 -f 2 -n 1 Trinity-GG.fasta > gmap_phaw.gff3

GMAP version 2020-06-01 called with args: gmap.sse42

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maria0



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