Question: Using HTseq and DEseq2 for RNAseq quantitation, format of input data?
gravatar for reubenmcgregor88
14 months ago by
reubenmcgregor8850 wrote:

Hi all,

For clarities sake my experimental setup is: 2 conditions (treated + non treated), with 3 replicated per condition.

This was sequenced using paired end Hiseq.

I mapped to reference genome using TopHat2 and counted the reads using htseq-count for all of the alignments separately.

I am about to run DESeq2 on these outputs.

Clearly my Factor1 and Factor 2 are treated and non treated respectively.

My qyesiotnv is ca I use a dataset collection as an input. So can I input the replicates as three input files, or do I have to somehow merge the replicated form the treatment and then the replicates from non-treated before inputting into DESeq2?

Please help!?



ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 14 months ago by reubenmcgregor8850
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Collections can be used (and is an accepted input type of the tool form). How-to is explained in the Galaxy tutorials here:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
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