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.h... Best, Jen Galaxy team On 4/17/12 8:00 AM, Ateequr Rehman 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
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