Hello All,
I would like to calculate RPKM for my single end read datasets. Initially I used cufflinks, but I am not satisfied with the results. So I thought I should try calculate RPKM manually. So I used bedtools to get number of reads covered for each gene. And then calculated RPKM using moratzavi formula. RPKM generated manually is largely differs from the cufflinks. I would really appreciate if anybody could provide explanation for this large difference?
And, I would like to know how cufflinks calculate coverage which it reports in the "Coverage" column in the isoforms_fpkm_tracking file? Because, it differs with bedtools too. for e.g, if bedtools report there are 10 reads covered for a specific gene, the cufflinks gives a non-integer number 199.079 under the coverage column. Why? Am I misinterpreting these metrics? Please correct me if I am wrong.
Thank you.
I would like to calculate RPKM for my single end read datasets. Initially I used cufflinks, but I am not satisfied with the results. So I thought I should try calculate RPKM manually. So I used bedtools to get number of reads covered for each gene. And then calculated RPKM using moratzavi formula. RPKM generated manually is largely differs from the cufflinks. I would really appreciate if anybody could provide explanation for this large difference?
And, I would like to know how cufflinks calculate coverage which it reports in the "Coverage" column in the isoforms_fpkm_tracking file? Because, it differs with bedtools too. for e.g, if bedtools report there are 10 reads covered for a specific gene, the cufflinks gives a non-integer number 199.079 under the coverage column. Why? Am I misinterpreting these metrics? Please correct me if I am wrong.
Thank you.