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Old 03-03-2016, 01:32 AM   #3
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 413
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Suggestions

#1 Remap reads to closely related genome. Satisfied with mapping rate ?

#2 Use gmap (easy) or Maker to map your de novo assembled transcripts to the related genome. Again, satisfied ? View both sets in a genome browser.

#3 if unsatisfied with #2 perhaps use Trinity genome guided or cufflinks to recreate transcripts.

#4 Quantify - ie using featureCounts - transcripts from #2 or #3.

Forget blast for this kind of approach.
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