Hi,
I'm looking for a method to give the read coverage for each gene. Our current method for making an RPKM cutoff is to manually look at our bedgraphs on UCSC Genome Browser and visually assess coverage. <----- Very tedious and subject to a number of flaws.
Ideally I would like to get a value for each gene that indicates how many bases are covered. i.e. 100% of all bases covered or 0%. Is there already something like this in BEDtools or an R package?
I use tophat to map and Seqmonk to count reads then manually calculate RPKM.
Thanks
Miguel
I'm looking for a method to give the read coverage for each gene. Our current method for making an RPKM cutoff is to manually look at our bedgraphs on UCSC Genome Browser and visually assess coverage. <----- Very tedious and subject to a number of flaws.
Ideally I would like to get a value for each gene that indicates how many bases are covered. i.e. 100% of all bases covered or 0%. Is there already something like this in BEDtools or an R package?
I use tophat to map and Seqmonk to count reads then manually calculate RPKM.
Thanks
Miguel
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