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Old 11-11-2015, 11:40 AM   #1
tellsparck
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Location: Philadelphia

Join Date: May 2012
Posts: 19
Default Refining cufflinks Gene models

Hi forum,
I suspect that my cufflinks denovo gene model set has many gene models antisense to known transcripts.When this model was use with featurecounts to count hits, I lose reads to many known genes and the unassigned _ambiguous class of reads go up, with unstranded libraries, but not stranded libraries. has any one tried to remove such artifactual gene models?
Thanks!
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