infering isoforms in merged transcriptome

[Fernando_Rodriguez]

Hi,

I assembled a transcriptome de-novo using the Evidential gene pipeline ( which merges multiple assemblies to generate a single transcriptome with high quality transcripts only ) and I would like to cluster my final transcripts to have isoform-gene associations.

I understand Evidential gene generates two files with main transcripts and alternative transcripts but the associations are not very clear to me so I would like to cluster the complete set of transcripts using read alignment information if possible. Does anyone knows of a software that does this ? If so, please let me know.

Thaks,
Fernando.

[dongilbert]

Fernando,

Find this answer in your evigene/docs/ folder, evgmrna2tsa_help.txt

Q: how do I create a gene-locus x transcript ID linking table, e.g.
gene1 transcript1
gene1 transcript2
gene2 transcript3

A: Use this script evgmrna2tsa2.pl, which is my recommended follow-on to tr2aacds.
$evigene/scripts/evgmrna2tsa2.pl -onlypubset -idprefix Aspecies1EVm -class aspecies.trclass

and for an overview of EvidentialGene uses, EvidentialGene_howto.txt

Web links are evigene/docs/evgmrna2tsa_help.txt
evigene/docs/EvidentialGene_howto.txt

-- Don Gilbert