View Single Post
Old 07-05-2012, 12:01 PM   #17
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 701

Sorry for a late response, vinay.
Those reads with no pair in the bam are "orphan reads". See the 05-10-2012 post for outputting orphan reads. "Good" bams should have all pairs whether mapped or not, though sometimes programs drop unmapped reads to save space.
Richard Finney is offline   Reply With Quote