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  • #1

    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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  • #2
    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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    • #3
      Wow...this is great. Thanks for passing it along!

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