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  • Stranger character in the quality scores column of sam files

    Hello everyone.

    I run bisulfite sequencing mapping with BSMAP. The output file was .sam format.
    But the quality scores look very strange. There were lots of unknown characters(I attached a picture)

    Here is the script:

    ./bsmap -a B4_ATGTCA_L00${i}_R1_00${j}.fastq -b B4_ATGTCA_L00${i}_R2_00${j}.fastq -d hg19.fa -o B4_ATGTCA_L00${i}_00${j}.sam -z 64 -v 15 -x 1000

    Did I do something wrong or set up wrong parameter?

    Thank you so much in advance!
    Attached Files

  • #2
    What happens if you don't use "-z 64". The manual for bsmap is wrong here, fyi (well, it's seriously outdated would be a better description).

    Comment


    • #3
      Originally posted by dpryan View Post
      What happens if you don't use "-z 64". The manual for bsmap is wrong here, fyi (well, it's seriously outdated would be a better description).
      It's works. Thank you so much!

      Comment

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