I am aligning paired end sequence reads using bwa mem and I get an error saying that paired reads have different names: "M01814:86:000000000-A6MU9:1:1101:15545:1335", "M01814:86:000000000-A6MU9:1:1101:16059:1338" So it looks like the locations for some of the reads don't quite match up. Is there a way to ignore these reads? Or to use them but not treat them as pairs?

  • $\begingroup$ are those Illumina reads? $\endgroup$ – Nandor Poka Jun 15 '15 at 21:44
  • $\begingroup$ Yes from the MiSeq $\endgroup$ – The Nightman Jun 15 '15 at 21:44
  • $\begingroup$ Ok, just wanted to confirm. Will look into it. $\endgroup$ – Nandor Poka Jun 15 '15 at 21:50
  • $\begingroup$ Do you have equal number of reads in your files (I assume you have separate files for the two ends). $\endgroup$ – Nandor Poka Jun 15 '15 at 22:05
  • $\begingroup$ Yep exact same number in each file. $\endgroup$ – The Nightman Jun 15 '15 at 22:13

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