This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to calculate RPKM using cuffdiff after obtaining accepted_hits.bam?

How to calculate RPKM using cuffdiff after obtaining accepted_hits.bam? Any suggestion will be appreciated. Thanks very much!

cuffdiff bam
• 3,992 views • link
updated by andrew.j.skelton73 andrew.j.skelton73 • written by biomoon • biomoon

1 answer

Follow the flowchart on this page

Edit: The Tuxedo pipeline uses FPKM metrics, not RPKM

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Thank you for your suggestion. Can you show me the command line of Cuffdiff with accepted_hits.bam and a genome reference GTF? Thanks a lot!

• 1 views • link
written by biomoon • biomoon

Regardless of that flow chart, is that possible that I only use genome reference GTF and bam file to get FPKM using only Cuffdiff? Show me if you know. Thanks.

• 0 views • link
written by biomoon • biomoon

Regardless of that flowchart - This is the manual for cuffdiff, which performs the statistical tests to calculate FPKM and perform differential expression from your alignments and gtf. All the command line arguments and options are there.

• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

I have seen that manual before I posted the disscussion. I am just curious how the author of one paper empoy Cufflink to calculate RPKM (or FPKM) in one software. The input of that software is alignment results of RNA-seq and a reference genome annotation. They may changed the algorithm. I think some people may know. Anyway, thank you for your reply! I appreciate it.

• 0 views • link
written by biomoon • biomoon

Cufflinks will calculate FPKM on a per sample basis, it's a transcriptome assembler, and a key element to that will be the quantification of how much stuff is assembled. I don't think the methodology has changed drastically, if at all - Cufflink's last update was its move to Github in 2014. Cufflinks outputs transcript and gene level FPKM tracking file, along with the GTF file.

• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Log in to answer this question.

More posts like this