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Old 02-21-2013, 03:17 PM   #1
jgibbons1
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Location: Worcester, MA

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Default FPKM/RPKM without GFF/GFT file

Hello all,
I had been using rseq and seqmap to calculate RPKM values for my transcriptome of interest. One of the benefits of this package is that is does not require a GFF/GTF file. I've moved to bowtie2 for my mapping and am curious if there is software available to calculate RPKM/FPKM without an associated GFF/GTF feature file. I've not been able to find this.
Thanks.
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Old 02-21-2013, 07:08 PM   #2
DWW1505
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Default re: FPKM/RPKM without GFF/GFT file

eXpress doesn't require a gtf and works well with Bowtie 1 and 2.
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Old 02-22-2013, 09:45 AM   #3
jgibbons1
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Wow...this is great. Thanks for passing it along!
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