Hi ! I have a table (58037×117) contain scaled read count for 117 sample (case and control) and gff and gtf file. Considering of RPKM calculation: RPKM=(row number of reads/exon length) ×(1000 000 / number of mapped reads in the sample) how can I get a table (58037×117) contain RPKM?? Is it solution based of use galaxy?
In the original publication by Ali Mortazavi et al. they provide the means to do so: http://www.nature.com/nmeth/journal/v5/n7/abs/nmeth.1226.html?foxtrotcallback=true
If you are searching for a more "divulgative" article on the topic, this is the most linked one: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/
Finally, a remark: I would suggest you to switch to TPM. Mortazavi himself suggested not to use RPKM anymore.
1) Enter "#" for your matrix header
2) Add one extra column to your matrix in the end (exon/gene length)
3) Use the following script according to the instructions,