Convert Trinity transcriptome assembly to GTF/GFF

[Atul Kakrana]

Hi List,

I know this issue is unrelated to Trinity, still it would be nice to have it documented here so that others in future can make use of it. How can we convert Trinity transcriptome assembly to GTF/GFF file?

If you can just tell me the steps in general, then I can maybe add the detailed answer. I guess it will need - mapping assembly (FASTA) to genome to get SAM file and converting SAM file to BED format. But how do we convert to proper GTF/GFF?

Atul

[Brian Haas]

If you want to align the assembled transcripts to a genome sequence and get GFF3 formatted output, you can use GMAP.  It has other output formats as well:

http://research-pub.gene.com/gmap/

If you want to do genome-based transcript reconstruction from the GMAP alignments, check out:

http://pasapipeline.github.io/

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Atul Kakrana]

Thanks for fast response. I will try these and post back.

Atul

Atul Kakrana
Delaware Biotechnology Institute