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Forum: Bioinformatics 10-21-2009, 05:08 AM
Replies: 1
Views: 5,039
Posted By rpm16
RPKM as calculated by TopHat

Does anyone have any experience with the RPKM (reads per kilobase of exon per million mapped reads) as calculated by TopHat? I can't find any documentation on how this is calculated, and I'm trying...
Forum: Bioinformatics 09-24-2009, 07:05 AM
Replies: 0
Views: 1,346
Posted By rpm16
Using Maq with TopHat

Is it possible to use Maq with the latest version of TopHat? I would like to use Maq to align my reads to a reference genome. Then I would like to use TopHat to call RPKM based on the Maq alignments...
Forum: Bioinformatics 05-12-2009, 11:53 AM
Replies: 0
Views: 1,443
Posted By rpm16
Maq map, only use part of the sequence

I am using maq's map program to map reads to a reference genome. I would like to use only the first 37bp of my reads (long story). I have used the -1 option, but I'm not sure I am using it correctly....
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