Question: What Kind Of Inputs Does Cuffdiff Take?
gravatar for narges
7.8 years ago by
narges180 wrote:


I have run tophat over the RNA-seq data and I got the output files : accepted_hits.bam, insertions.bed, junctions.bed, deletions.bed, unmapped.bam.

Now to find the DE genes I want to run cuffdiff over the results. Is it enough if I use the accepted_hits.bam files + gtf file as the inputs for cuffdiff or I need to also use any other output files from tophat as well? For example do I need to have accepted_hits.bam + insertions.bed or junctions.bed for each samples?

Thank you in advance

tophat cuffdiff • 3.4k views
ADD COMMENTlink modified 7.7 years ago by blair20 • written 7.8 years ago by narges180
gravatar for Istvan Albert
7.8 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

From the manual:

Cuffdiff takes a GTF2/GFF3 file of transcripts as input, along with two or more SAM files containing the fragment alignments for two or more samples.

ADD COMMENTlink written 7.8 years ago by Istvan Albert ♦♦ 85k
gravatar for blair
7.7 years ago by
Cambridge, MA
blair20 wrote:

The BED output files produced by TopHat are for those interested in discovering new transcripts and splice-junctions. For a DE experiment using samples from an organism with a well annotated genome (like human or mouse) then your best bet is to just take your accepted_hits.bam from TopHat and input it right into Cuffdiff along with a reference GTF/GFF (the ones from iGenomes are nice because they extra annotations like TSS that are needed to get full alternative splicing info from your data). Hope that helps!

ADD COMMENTlink written 7.7 years ago by blair20

Hello! Can you show me the command line of Cuffdiff with accepted_hits.bam and a genome reference GTF? What I want to get is RPKM or FPKM. Thank you a lot!

ADD REPLYlink written 4.7 years ago by biomoon10
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