Help with Exonerate output

mycorr10 · 02-06-2012, 02:50 PM

I'm doing some cdna to genomic dna alignments with exonerate but am having trouble parsing the output- not very good at that sort of thing.
I would like the gff and alignment as separate files. In particular does anyone know how to input the ryo option to make the alignment more like a basic fasta formatted alignment? I'd like to combine the results and make a multiple sequence alignment I can edit and view to make a consensus sequence.

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02-06-2012, 02:50 PM	#1
mycorr10 Junior Member Location: France Join Date: Dec 2011 Posts: 7	Help with Exonerate output I'm doing some cdna to genomic dna alignments with exonerate but am having trouble parsing the output- not very good at that sort of thing. I would like the gff and alignment as separate files. In particular does anyone know how to input the ryo option to make the alignment more like a basic fasta formatted alignment? I'd like to combine the results and make a multiple sequence alignment I can edit and view to make a consensus sequence.