Question: Cuffdiff
gravatar for Vevis, Christis
6.0 years ago by
Vevis, Christis30 wrote:
Hi, I got confused while trying to perform Cuffdiff for my RNA sequencing analysis. So I have five different samples which were sequenced. I used tophat to create the bam files and cufflink to create the assembled trancripts. Then I uded Cuffmerge to merge them in one file and then I wanted to do Cuffdiff with that merged file. What shall I choose for the ''SAM or BAM file of aligned RNA-Seq'' option? I have the 5 options from the 5 tophat actions on my 5 samples. All I want in the end is an excel table showing the number of hits from each sample (and not necessary a comparison of them). Regards Kristis Vevis, PhD Student Cell Biology UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL, UK 020 7608 4067
rna-seq cuffmerge • 1.0k views
ADD COMMENTlink modified 6.0 years ago by Jeremy Goecks2.2k • written 6.0 years ago by Vevis, Christis30
gravatar for Jeremy Goecks
6.0 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Use the replicates option (yes, a bit of a misnomer) and put each Tophat run in its own group. This will produce a tabular file with FPKM for each group/run. Best, J.
ADD COMMENTlink written 6.0 years ago by Jeremy Goecks2.2k
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