SEQanswers - View Single Post - Best way to search for gene homologue in metagenomic dataset

rhinoceros · 10-08-2013, 05:48 AM

I'm confused. Your question implies that you have a WGS metagenome but then you use the word amplicon. Anyway, maybe you could do a reference guided assembly using your favorite gene as a reference? Alternative you could map your reads against a representative set of your favorite gene and then assemble those reads? There are so many ways to do this..

10-08-2013, 05:48 AM	#2
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	I'm confused. Your question implies that you have a WGS metagenome but then you use the word amplicon. Anyway, maybe you could do a reference guided assembly using your favorite gene as a reference? Alternative you could map your reads against a representative set of your favorite gene and then assemble those reads? There are so many ways to do this.. __________________ savetherhino.org Last edited by rhinoceros; 10-08-2013 at 05:51 AM.