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What Kind Of Inputs Does Cuffdiff Take?

Hi,

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

cuffdiff tophat
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updated by blair • blair • written by narges • narges

2 answers

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.

http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_input

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written by Istvan Albert Istvan Albert

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!

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written by blair • blair

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!

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written by biomoon • biomoon

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