infering isoforms in merged transcriptome

Fernando_Rodriguez · 01-28-2019, 08:08 AM

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 · 01-29-2019, 10:20 AM

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

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01-28-2019, 08:08 AM	#1
Fernando_Rodriguez Junior Member Location: starkville Join Date: Jan 2019 Posts: 1	infering isoforms in merged transcriptome 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.

01-29-2019, 10:20 AM	#2
dongilbert Junior Member Location: indiana Join Date: Jun 2012 Posts: 9	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