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Old 09-08-2014, 03:29 AM   #1
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Location: Norway

Join Date: Jul 2009
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Default Using transcdecoder on de novo transcriptome


About de novo transcriptome. I know blastx is very time consuming (on 150.000 seqs), and got a suggestion to first use CD-HIT EST (too reduce redundancy), then transdecoder to convert to peptides and then blastp against ref-seq protein database to speed up transcriptome annotation. So far so good, but I have some problems.

How to you normally proceed after transdecoder, when many cDNA contigs has several ORFs? Then each cDNA contig could have several annotations. I usually import the blast xml to Blast2go, and would like to only use one (best hit) annotation per cDNA contig for further analysis of the transcriptome.

Any suggestions?

Cheers Erik
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