[Transdecoder-users] Transcoder question

[Erik L. <eri...@bi...>]

Dear developers

About de novo transcriptome. I know blastx is very time consuming, 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