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Old 01-28-2019, 08:08 AM   #1
Fernando_Rodriguez
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Location: starkville

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Default 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.
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Old 01-29-2019, 10:20 AM   #2
dongilbert
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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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evidential gene, isoform clustering, merging transcriptomes, transcriptomics

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