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Old 08-28-2014, 11:13 PM   #1
Location: italy

Join Date: Sep 2010
Posts: 55
Default Bwa, sampe vs samse

Hi guys,

this is probably a silly question. If I run bwa sampe I will get an alignment file which report informations about the paired end reads being in the expected pairing mode on the reference genome. However also not properly mapped paired reads will be reported, such as reads that maps although the mate does not map. Does this mean that the alignment sam file will provide the same information reported by the sam file generated by bwa sampe?
If I run sampe with paired end reads I am treating all the reads as unpaired and I will map them on the reference. Since for samse I will map the reads even if they are unpaired I would expect the same result than samse. Am I correct?
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Old 08-29-2014, 12:48 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

I'm guessing that you swapped "sampe" and "samse" a few times in your post.

In general, if a pair are aligned as singletons with sampe then they should be given the same alignment with samse. The only difference with by the FLAG field, since in one case they would have been paired in sequencing (bit 0x1) and have had an order (bits 0x40 and 0x80), though obviously bit 0x2 would be unset.
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Old 08-29-2014, 01:16 AM   #3
Location: italy

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Thanks a lot! Yes sorry I used sampe and samse all the way around. You answer clarifies everything.
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