Question: Can standard CuffDiff output be used as input into CummeRbund on Galaxy?
gravatar for connorrogerson
21 months ago by
connorrogerson0 wrote:

I've been analysing some RNA-seq data in triplicate and I want to compare replicates by generating scatter plots. This can be done by CummeRbund but I have little experience with R and Galaxy has usually helped me out in these situations. However, the Galaxy version of CummeRbund insists on a SQlite database but I analysed my RNAseq using Cufflinks on my local machine so I didn't have the option of ticking a box for SQlite output. Can CummeRbund on Galaxy function with standard Cuffdiff output? And if so how can this work on Galaxy?

ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by connorrogerson0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The cummeRbund tool as wrapped for Galaxy requires the SQlite input. Perhaps rerun the analysis in Galaxy to generate the proper inputs?

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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