[BioC] how to create a TranscriptDb object from bed file

Ann Loraine aloraine at gmail.com
Tue Sep 7 06:56:08 CEST 2010


I have a "bed" format file containing model gene annotations from a
plant genome and would like to convert this into
a TranscriptDb object so that I can use EdgeR to count overlapping
reads from an RNA-Seq experiment.

Are there some tools available that can read the 'bed' file and
produce a TranscriptDb object?

I'm looking at the documentation on p. 6 in:


What is "exon rank?" Is this the order an exon appears in a transcript?

If gene A is on the minus strand, is this the correct ranking of its exons,
 or does it matter?

    1               2                 3

Does TranscriptDb assume 1-based or interbase coordinates?

Very best wishes,

Ann Loraine

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