Cuffdiff

Question: Cuffdiff

6.6 years ago by

Ateequr Rehman • 150 wrote:

Dear All I have simple and question for cuffdiff should we run cuffdif on merge transcript file (produced by cuffmerge) and concatenate data sets or directly on cufflink produced files, in the later case, i have two transcript files resulting from cufflink on sample 1 and 2 respectively, result using sample 1 as transcripts are not the same when i am suing sample 2 as transcript i am bit confused what should be the correct way any help is very much welcomed Best ateeq Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau

rna-seq cuffmerge • 1.1k views

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modified 6.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.6 years ago by Ateequr Rehman • 150

6.6 years ago by

Carlos Borroto • 390

Washington Metropolitan Area

Carlos Borroto • 390 wrote:

Hi Ateequr, I don't think there is an easy answer to your question. I would highly recommend you take a look to this recently released paper from Tophat and Cufflinks authors: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. http://www.ncbi.nlm.nih.gov/pubmed/22383036 The somehow short answer to your question is, you should run cuffdiff with the transcript file from cuffmerge, although I don't quite understand what you mean by "and concatenate data sets". You should not concatenate the BAM files, or you won't be able to run cuffdiff correctly. Depending on how you ran cufflinks, by using the transcript file from cuffmerge you will get expression values for possible new transcripts not present in the databases. This is commonly desired. If you aren't interested in possible new transcripts, then you could simply use a GFF file with transcripts definitions for the genome you are using. In this case you will have the advantage of getting the results with IDs compatibles with the database source the GFF came from. If you use the cuffmerge file you might have the results using cufflinks generated IDs. Hope it helps, Carlos

ADD COMMENT • link written 6.6 years ago by Carlos Borroto • 390

6.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Ateequr, This post from today has information another member found at seqanswers.com, directly from the CuffLinks/Merge/Diff tool author: http://user.list.galaxyproject.org/Re-1-cuffcompare-or-cuffmerge- td4581029.html Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

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