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Forum: RNA Sequencing 03-08-2016, 12:27 AM
Replies: 8
Views: 3,589
Posted By colindaven
A GMAP command which produces GFF3 output might...

A GMAP command which produces GFF3 output might look like this:

~/gmap-2015-07-23/bin/gmap -f gff3_gene -D gmap/ -d mygenome.fasta.gmap -B 5 -t 12 --intronlength=50000 --totallength=1000000 -p 3...
Forum: RNA Sequencing 03-03-2016, 02:32 AM
Replies: 8
Views: 3,589
Posted By colindaven
Suggestions #1 Remap reads to closely...

Suggestions

#1 Remap reads to closely related genome. Satisfied with mapping rate ?

#2 Use gmap (easy) or Maker to map your de novo assembled transcripts to the related genome. Again, satisfied...
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