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infering isoforms in merged transcriptome

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  • 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.

  • #2
    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

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