i am working with pair end & single end transcriptome, I have FPKM for pair end data using FPKM count tools in galaxy, but for single end data I need RPKM value, how can I get that?
someone said the cufflinks can help, i used cufflinks and now have FPKM value in my data, but my data was single end! and for single end data the RPKM value should be compute, my question is: Is this FPKM value for single end data equal to RPKM?
How can i compute RPKM value for single end data in galaxy?
Hi @Dr.Lida
For SE data RPKM should be identical to FPKM (a read is equal to a fragment).
It is a little bit complicated for PE data. If both F and R reads are mapped to a gene, the reads are counted as one fragment. Then there are complicated cases, for example, when only one read is mapped, or reads are mapped to different genes or not properly paired, e.g., mapped to different chromosomes. If only one read from a pair is mapped, usually the read corresponds to a fragment. I don’t know how not properly paired reads are treated.
Hope this helps.
Kind regards,
Igor