Re: [galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

different, then you very likely have different populations in the two files. Good luck with your project! Jen Galaxy team On 1/7/13 1:47 PM, Wei Liao wrote: Hi all, I am analyzing significant differential expressed genes for a pair of normal V.S tumor, using Cuffdiff 2.0.2. I noticed

[galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

genes differential expressed. But for refseq GTF, there are about 1000 genes. I am running these data on Galaxy server and with the same workflow. Can anyone explain what is going on here? so which result should I trust? Thanks. -- Wei Liao Research Scientist, Brentwood Biomedical Research

[galaxy-user] Tophat alignment statistics?

. -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

[galaxy-user] Cuffdiff tracking file does not report all genes and trancrips from reference annotation?

only compare 2000 genes and 4000 transcripts between samples. The question I want to ask here is that *why are the rest of the genes and transcripts not being tested and included in the tracking files?* Do you know what cause this kind of problem? Thanks, Wei -- Wei Liao Research Scientist, Brentwood

Re: [galaxy-user] 1. cuffcompare or cuffmerge (???)

feel that option #3 is actually the most accurate in most experimental settings. Hope this helps. Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645 Today's Topics: 1. cuffcompare or cuffmerge