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?
thanks
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?
thanks
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