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  • #16
    Originally posted by id0 View Post
    You can try trimming your FASTQ files and see how that goes. Sickle trims based on quality scores, so you would only lose low quality bases:
    https://github.com/najoshi/sickle
    We'll give that a try. Thanks!

    Comment


    • #17
      Originally posted by id0 View Post
      My original BWA issue did not get resolved. I am using Mac OS X 10.7 and I have seen reports of other Mac users reporting the same problem. When I switched from BWA 0.6.2 to BWA 0.5.9, it was working fine.

      As I was writing this reply, I noticed BWA 0.7.0 was released last week. I am not sure if that one solves any of the Mac issues. See changelog here:
      Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) - File not found · lh3/bwa




      I used BWA for 2x250bp reads and I did not encounter any problems. From BWA main page:
      hi,
      It looks like the last 3 versions of bwa, including the latest released last week, don't work on a Mac. I downloaded 0.5.10 and I think things are working now. It's definitely taking much longer to make the .sai file, so I see that as a good sign.
      Thanks!

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      • #18
        I just ran into this after I aligned human paired-end sequences against the tiny non-human genome included in the distribution kit.
        Opps:-(
        Bill

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