SEQanswers - View Single Post - V4-V5 Region Using 2x250

pmiguel · 03-13-2018, 12:24 PM

I think the critical factor is that at a cluster density where you produce the most sequence (even the most Q30 bases), the quality of single-plex amplicon runs deteriorates badly over the last 50 bases of a 250 cycle read. Whereas if you keep the density much lower--such that you may only generate 10 million or fewer clusters--the quality can be high all the way to the ends of the reads.

At these lower cluster densities we see pair merging occurring successfully at rate approaching 90% even with 450bp inserts.

600 cycle cassette? I don't know, is anyone getting reasonable 300 base reads with those?

--
Phillip

03-13-2018, 12:24 PM	#2
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	I think the critical factor is that at a cluster density where you produce the most sequence (even the most Q30 bases), the quality of single-plex amplicon runs deteriorates badly over the last 50 bases of a 250 cycle read. Whereas if you keep the density much lower--such that you may only generate 10 million or fewer clusters--the quality can be high all the way to the ends of the reads. At these lower cluster densities we see pair merging occurring successfully at rate approaching 90% even with 450bp inserts. 600 cycle cassette? I don't know, is anyone getting reasonable 300 base reads with those? -- Phillip