Skip to content

Gtf file #212

@luisafmc

Description

@luisafmc

Hello,
Thank you so much for the development of RSEM.
I am trying to run the RSEM in a non model species, however after many trials I having issues with the gtf. If it is possible I will like to ask which kind of information should be contained in the gtf. My actual gtf have an structure of 9 genes where one have two types of transcript (in total 10 entries).

The entries are like the following (one gene example):
##gff-version 3
Chr_scaffold_ancX GINGER CDS 62941173 62949964 . + . gene_id "Cdx4.cds1";transcript_id "Cdx4.mrna1";
Chr_scaffold_ancX GINGER mRNA 62941173 62949964 . + . gene_id "Cdx4.mrna1";transcript_id "Cdx4.mrna1";
Chr_scaffold_ancX GINGER gene 62941173 62949964 . + . gene_id "Cdx4.mrna1";transcript_id "Cdx4.mrna1";
Chr_scaffold_ancX GINGER exon 62941172 62941837 . + . gene_id "Cdx4-exon1";transcript_id "Cdx4.mrna1";
Chr_scaffold_ancX GINGER exon 62947725 62947870 . + . gene_id "Cdx4-exon2";transcript_id "Cdx4.mrna1";
Chr_scaffold_ancX GINGER exon 62949186 62949964 . + . gene_id "Cdx4-exon3";transcript_id "Cdx4.mrna1";

Could you gimme some hints about the structure need it to run the program?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions