Question: Output normalized RNA-seq data from DESeq2
0
gravatar for richard.radcliffe
17 months ago by
United States
richard.radcliffe0 wrote:

Hello-

Is it possible to out put the normalized data from RNA-seq DEXSeq2 analysis? I don't see anything that would allow one to do that.

Thanks.

ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson24k • written 17 months ago by richard.radcliffe0
0
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The tool as wrapped in Galaxy outputs the mean of normalized counts across samples, as described on the tool form. A distinct dataset with the raw normalized counts is not created by the tool using the implemented functions.

If you want to parse the data for this information, there are several line command options described on other boards, including https://www.biostars.org. Try a google search to find these and others and review.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson24k

Thanks for the speedy response. Do you mean using the command line options on my own Galaxy instance (which I don’t have) or is there a way to use the command line on the public Galaxy server?

ADD REPLYlink written 17 months ago by richard.radcliffe0

I meant command line itself (not in Galaxy), such as a terminal window.

ADD REPLYlink written 17 months ago by Jennifer Hillman Jackson24k

Got it – thanks.

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Monday, November 14, 2016 3:09 PM To: Radcliffe, Richard Richard.Radcliffe@ucdenver.edu Subject: [galaxy-biostar] Output normalized RNA-seq data from DESeq2

Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org

User Jennifer Hillman Jacksonhttp://biostar.usegalaxy.org/u/254/ wrote Comment: Output normalized RNA-seq data from DESeq2http://biostar.usegalaxy.org/p/20513/#20519:

I meant command line itself (not in Galaxy), such as a terminal window.

ADD REPLYlink written 17 months ago by richard.radcliffe0

Update: The latest version of DESeq2 (Galaxy Version 2.11.38) has a new form option to output the normalized counts as a tabular file. This is brand new as of last night. We are still testing the install - and will tune it to get it right (prior version had some bugs), but you can try it now or follow this ticket to learn when it is definitively ready to use at http://usegalaxy.org: https://github.com/galaxyproject/tools-iuc/issues/988

ADD REPLYlink written 17 months ago by Jennifer Hillman Jackson24k

Great – thanks very much for the update.

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Wednesday, November 16, 2016 10:07 AM To: Radcliffe, Richard Richard.Radcliffe@ucdenver.edu Subject: [galaxy-biostar] Output normalized RNA-seq data from DESeq2

Activity on a post you are following on Galaxy Biostarhttp://biostar.usegalaxy.org

User Jennifer Hillman Jacksonhttp://biostar.usegalaxy.org/u/254/ wrote Comment: Output normalized RNA-seq data from DESeq2http://biostar.usegalaxy.org/p/20513/#20548:

Update: The latest version of DESeq2 (Galaxy Version 2.11.38) has a new form option to output the normalized counts as a tabular file. This is brand new as of last night. We are still testing the install - and will tune it to get it right (prior version had some bugs), but you can try it now or follow this ticket to learn when it is definitively ready to use at http://usegalaxy.org: https://github.com/galaxyproject/tools-iuc/issues/988

ADD REPLYlink written 17 months ago by richard.radcliffe0
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