Question: Deseq2 usage Galaxy
2
gravatar for k.makwana
3 months ago by
k.makwana20
k.makwana20 wrote:

Hello, I am trying to do some differential expression count on RNA Seq data using Galaxy. I did an alignment to reference genome and uploaded the files on the galaxy and did HTseq count and then Deseq2. My experiment set up is such that I have 6 duplicate samples for control and 6 duplicate for experimental group collected at 6-time points across the 24hr cycle(2hr, 6hr,10hr,14hr,18hr,22hr). So while using Galaxy I chose Factor level 1 as control and selected all the control file and did same for the experimental group. I have to further analyze these data to look out for the genes those were having circadian rhythms upon treatment. So I checked for normalized read counts generated by Deseq2. Here lies the problem, The results show normalized values for both groups labeled as 1,2,3,4....12 (Control 1, control2......control12, experimental 1, experimental 2.......experimental 12). I need precise values for every time point in order to see which all genes are expressed in a circadian manner. Is there any way to do this?

Thanks for your help.

ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by k.makwana20
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

A change was just made to the tool to name the headers in a more informative way.

The updated tool (DeSeq2, Galaxy Version 2.11.40.1 https://toolshed.g2.bx.psu.edu/view/iuc/deseq2/3660c9088494) can be installed in your own local/cloud/docker Galaxy https://galaxyproject.github.io/ or use it now at the public server Galaxy EU https://usegalaxy.eu/.

The latest version is not yet available at the public server Galaxy Main https://usegalaxy.org. Ticket for the tool update (follow for status): https://github.com/galaxyproject/usegalaxy-playbook/issues/101

Details, if interested:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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