I am new to using Galaxy tools. I am running paired end RNA-Seq data on
Galaxy and I want to differential gene expression between control and
I was fine until running TopHat output, I am having problems with cufflinks
and cuffdiff output.
I ran the cufflinks and cuffdiff twice, once with reference annotation and
once without reference annotation (Imported form UCSC).
Output with reference annotation produced output with gene ids naming usc##
Output without reference annotation produced output with gene ids naming
Can anyone suggest how to get gene names instead of just numbers?
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