How to calculate RPKM after tophat mapping

Dear all

I performed tophat mapping, and generated accepted_hits.bam file. Next, how to calculate RPKM according to this file? Do I have to write a script myself to complete this job? Any suggestions will be appreciated. THANKS in advance.

rpkm tophat

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updated 4.4 years ago by Ram

• written 11.6 years ago by biolab

1 answer

I guess if you follow the protocol that I showed you on your other post, after doing cuffdiff, it will produce a file diff_out that you can find FPKM in it.

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updated 4.4 years ago by Ram

• written 11.6 years ago by Parham

Hi Parham, thanks a lot for your comments! From one PhD thesis, I learned RPKM can be calculated directly after tophat, without cufflinks step, but the author did not describe in details the calculation. Do you have any ideas for his approach? Thanks again.

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updated 4.4 years ago by Ram

• written 11.6 years ago by biolab

Hi, no I have no idea. But running Tuxedo won't take much time and by having Nature protocol it is very straight forward.

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updated 4.4 years ago by Ram

• written 11.6 years ago by Parham

Hi, Parham, thanks a lot for your comments!

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updated 4.4 years ago by Ram

• written 11.6 years ago by biolab

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