SEQanswers - View Single Post - cross species RNA-seq/orthologs

colindaven · 05-19-2016, 04:27 AM

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.

05-19-2016, 04:27 AM	#2
colindaven Senior Member 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.