Mate Pair Alignment Summary
Hi all, I have vague memories of running an aligner on mate-pair data and having it generate a summary of how many read pairs made proper mate-pairs, paired ends, or unexpected orientations.
Can anyone tell me if they know of an aligner that does this?
1 answer
Log in to answer this question.
More posts like this
-
What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
written by William
-
Mate pairs and paired reads confusion
written by Joel Wallenius
-
Why do paired ends map to same coordinates of a scaffold?
written by wmorgan •
-
Does 5' read trimming affect duplicate detection?
written by mcrepeau •
-
Determining Paired-end or Mate-pair insert length in De Novo Sequencing
written by sameedmsiddiqui •
-
Assembly with mate-pairs issue
written by lieven.sterck
-
SAM flags meaning
written by lilach.kornblitno •
-
Question about strand orientation.
written by mangfu100
-
Proper Bam / Tophat Output For Strand Specific Paired-End Data?
written by user
-
How To Differentiate Between Mate Pair And Paired End Reads Based On Sam Flag
written by Abhi
run samtools flagstat on the alignment bam file
Consider converting this from a comment to an answer so that others can see that the question has been answered?