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  • ahli1981
    Member
    • Sep 2011
    • 10

    #1

    how to know a gene's strand

    Hi all, is there any file recording whether a gene is on the + strand or the - strand?

    Ultimately I want to know a position (chr coordinate) is within which exon of the gene, but I do not know the phase information of that gene, so I cannot judge the exon index (increasing with increasing coordinate or decreasing with increasing coordinate)

    Thanks.
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    For many genomes, there exists a GFF or GTF file describing exon coordinates and strands. Examples (from Ensembl) are here.

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