SEQanswers - View Single Post - Enable pairing in a bam file separately aligned by lanes

GenoMax · 02-11-2016, 12:17 PM

Aligning sequences in pairs provides spatial context to aligners (not sure which one you used). Just do the alignment again this time using both reads. You can then merge the resulting bam files if the same sample ran in more than one lane.

02-11-2016, 12:17 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Aligning sequences in pairs provides spatial context to aligners (not sure which one you used). Just do the alignment again this time using both reads. You can then merge the resulting bam files if the same sample ran in more than one lane.