[BioC] how to create a TranscriptDb object from bed file
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,
More information about the Bioconductor