I tried to follow the Cufflinks tutorial created by Jeremy. The
problems start with first "visualization" step. The is no overlapping
at all between Cufflinks transcripts and RefSeq Chr19 reference,
provided on the tutorial page. Was that the goal, or transcripts
should overlap and something did not work? By the way, mapping for
cufflinks was done to hg19, but reference annotation is provided at
hg18. Maybe, this is the problem?
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