Confusing Output of Mate/paired Mapping

  • Nathan S. Watson-Haigh

    I liked the output stats regarding the number of mapped, multi-mapped and unmapped reads when mapping single-end/shotgun reads. However, It took me a while figure out the numbers for mates I was mapping as the output is somewhat more complicated and convoluted. Could I suggest that the output is changed to something like:

    xxx reads; of these:
      xxx (x%) were discarded on input
      xxx (x%) were paired; of these pairs:
        xxx (x%) aligned concordantly exactly 1 time
        xxx (x%) aligned concordantly >1 times
        xxx (x%) aligned concordantly exactly 1 time
        xxx (x%) aligned discordantly >1 times
        xxx (x%) had one or both mates unaligned; of these:
         xxx (x%) aligned 0 times
         xxx (x%) aligned exactly 1 time
         xxx (x%) aligned >1 times

    I think this makes it clearer how many were mappable as pairs, of those which were concordant and discordant, those which were not mapped as pairs and those which were not mapped at all.

    My $0.02 worth :)

  • Nathan S. Watson-Haigh

    spot the typo!

  • Nobody/Anonymous

    i was trying to align paired end reads to human genome, i was  not able to get the correct sam alignment as i dint even receive the sam file summary at the end.


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