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Old 06-23-2011, 09:42 AM   #1
apratap
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Location: Bay Area

Join Date: Jan 2009
Posts: 58
Smile BWA behaviour with Mate Pair data + Multi read mapping

Hi All

PS: This message was also posted on BWA mailing list but I did not get any response.


I am not able to logically understand why BWA is/not able to work natively
with mate pair data. Second question is whats the best work around if I
want to obtain multiple read mappings (if any) for a read. I am also pasting
the result of aligning mate pair data both before and after reverse
complimenting. The mapping gets better after rev comp but I dont quite
understand why. Appreciate you input on both my questions.


A. Before Reverse comp : Mate pair data <----- ------>

356766 + 0 in total (QC-passed reads + QC-failed reads)
282236 + 0 mapped (79.11%:nan%)
356766 + 0 paired in sequencing
178383 + 0 read1
178383 + 0 read2
126094 + 0 properly paired (35.34%:nan%)


B. After Reverse Comp : Mate pair data --------------->
<----------------------

356766 + 0 in total (QC-passed reads + QC-failed reads)
265575 + 0 mapped (74.44%:nan%)
356766 + 0 paired in sequencing
178383 + 0 read1
178383 + 0 read2
11146 + 0 properly paired (3.12%:nan%)


It seems the algo takes a major hit during the pairing of reads.

Thanks!
-Abhi
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