Re: [galaxy-user] How to get reads counts from cufflins?

2012-02-08 Thread Li, Jilong (MU-Student)
ictor From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Thursday, February 09, 2012 4:00 AM To: Li, Jilong (MU-Student) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to get reads counts from cufflins? Victor, I got the normalized values (FPKM)

[galaxy-user] How to get reads counts from cufflins?

2012-02-08 Thread Li, Jilong (MU-Student)
Hi all, I got the normalized values (FPKM) from cufflinks. And I want to get relative reads counts. How can I do that? Another question: how does cufflinks handle isoform genes while calculating the reads counts? Or what papers can help me understand this? Thank you very much! Victor

[galaxy-user] about Mapping Quality

2012-02-07 Thread Li, Jilong (MU-Student)
Hi all, I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the value of some mapping quality (the 5th column) is 255. What does it mean? And I found these reads which have mapping quality 255 mapped to unique place. Thanks! Victor

[galaxy-user] cufflinks FPKM

2011-11-03 Thread Li, Jilong (MU-Student)
Hi, I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the expression data. I think FPKM is for pair-end reads. right? My reads are single-end. Is it right if I use FPKM? Thank you very much! Victor ___

Re: [galaxy-user] how to transfer gene id into protein id

2011-10-28 Thread Li, Jilong (MU-Student)
From: Jennifer Jackson [j...@bx.psu.edu] Sent: Thursday, October 27, 2011 11:23 PM To: Li, Jilong (MU-Student) Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] how to transfer gene id into protein id Hello, If the reference genome is in UCSC and has a RefSeq track, then you can extract a

[galaxy-user] how to transfer gene id into protein id

2011-10-27 Thread Li, Jilong (MU-Student)
Hi, I have some refseq gene id, like NM_*. How can I transfer these gene id into protein id, like NP_? Thank you very much! Victor ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on

[galaxy-user] FW: one error while installing galaxy

2011-10-21 Thread Li, Jilong (MU-Student)
Hi, When I installed galaxy, one error message appeared, which said that ImportError: No module named distutils.util Fetch failed. Could you tell me how to solve this problem? Thank you very much! ___ The Galaxy User list should be used for

[galaxy-user] one error while installing galaxy

2011-10-19 Thread Li, Jilong (MU-Student)
Hi, When I installed galaxy, one error message appeared, which said that ImportError: No module named distutils.util Fetch failed. Could you tell me how to solve this problem? Thank you very much! ___ The Galaxy User list should be used for