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Old 05-19-2016, 04:27 AM   #2
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Location: Germany

Join Date: Oct 2008
Posts: 415

Do you have a genome ? Where do you get your sequences from if not, transcript de novo assemblies ?

I would suggest proteinortho instead of orthomcl, as it is simpler in my experience.

I would use STAR instead of tophat2 if possible, featureCounts for read counting and edgeR/DEseq2 for DE analysis if it all works out.
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