[galaxy-user] How to get reads counts from cufflins?
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 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to get reads counts from cufflins?
Victor, I got the normalized values (FPKM) from cufflinks. And I want to get relative reads counts. How can I do that? It's not clear to me what you're looking for. FPKM is a normalized read count metric where the F stands for fragment, which is a single read (or half of a paired read). Another question: how does cufflinks handle isoform genes while calculating the reads counts? Or what papers can help me understand this? Expectation maximization is used to probabilistically assign reads to isoforms. See the Cufflinks documentation for details and paper links: http://cufflinks.cbcb.umd.edu/ Best, J.___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to get reads counts from cufflins?
Dear Jeremy, Sorry, I didn't expressed my question clearly. I got the FPKM normalized values for each gene from cufflinks. And I want to get the original reads counts that were not normalized from cufflinks. Could you please tell me how to get those? Thank you very much! Victor 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) from cufflinks. And I want to get relative reads counts. How can I do that? It's not clear to me what you're looking for. FPKM is a normalized read count metric where the F stands for fragment, which is a single read (or half of a paired read). Another question: how does cufflinks handle isoform genes while calculating the reads counts? Or what papers can help me understand this? Expectation maximization is used to probabilistically assign reads to isoforms. See the Cufflinks documentation for details and paper links: http://cufflinks.cbcb.umd.edu/ Best, J. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to get reads counts from cufflins?
Reads are probabilistically assigned, so raw read counts are not available from Cufflinks. Recovering raw fragment counts could be done by reverse-engineering the FPKM value, but Cufflinks doesn't do this for you. If you choose to do this, keep in mind that Cufflinks uses an effective transcript length. Best, J. On Feb 8, 2012, at 11:06 PM, Li, Jilong (MU-Student) wrote: Dear Jeremy, Sorry, I didn't expressed my question clearly. I got the FPKM normalized values for each gene from cufflinks. And I want to get the original reads counts that were not normalized from cufflinks. Could you please tell me how to get those? Thank you very much! Victor 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) from cufflinks. And I want to get relative reads counts. How can I do that? It's not clear to me what you're looking for. FPKM is a normalized read count metric where the F stands for fragment, which is a single read (or half of a paired read). Another question: how does cufflinks handle isoform genes while calculating the reads counts? Or what papers can help me understand this? Expectation maximization is used to probabilistically assign reads to isoforms. See the Cufflinks documentation for details and paper links: http://cufflinks.cbcb.umd.edu/ Best, J. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
