Low Concordance HiSAT2

Question

[willthompson131]

Hey y'all,

I'm trying to QA a de-novo transcriptome assembly of an ambystomid salamander. When I use HiSAT2 the reads (2x75 bp) I used to make the assembly back to the assembly, I get very high lack of concordance (0.17%). When I map my reads used to construct the assembly back to the assembly, I get this:

 96120217 reads; of these:
  96120217 (100.00%) were paired; of these:
    95936608 (99.81%) aligned concordantly 0 times
    164062 (0.17%) aligned concordantly exactly 1 time
    19547 (0.02%) aligned concordantly >1 times
    ----
    95936608 pairs aligned concordantly 0 times; of these:
      11445015 (11.93%) aligned discordantly 1 time
    ----
    84491593 pairs aligned 0 times concordantly or discordantly; of these:
      168983186 mates make up the pairs; of these:
        32399441 (19.17%) aligned 0 times
        52185177 (30.88%) aligned exactly 1 time
        84398568 (49.94%) aligned >1 times
83.15% overall alignment rate

Any thoughts would be greatly appreciated!

[Devon Ryan]

Did the paired-end files become out of sync at some point?