Tuxedo Pipeline with single condition

[Daytwa]

I've been asked to run a deep coverage mouse RNA-seq sample through the Tuxedo pipeline as this analysis tool has been used before in the lab. However, we are only looking to determine expression levels and discover new transcripts. We do not want to perform differential expression analysis. In other words RNA from an as yet unsequenced call type was sequenced and was not part of a treatment/control or condition1/condition2 paradigm. I had doubts about the usefulness of Tuxedo for this sample after reading the corresponding literature but took the analysis through the Tophat-> Cufflinks -> Cuffmerge anyways.

Can FPKM values be generated from the Cuffmerge results without performing differential analysis? Would Cuffcompare be the better script to filter out the artifact transfrags?

[sindrle]

Hows this going?