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  • Yvone
    replied
    Originally posted by Rui View Post
    I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.
    The deleted bases will be presented as ‘*’ in the following lines.

    Leave a comment:


  • Rui
    replied
    I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.

    Leave a comment:


  • hanleng
    replied
    Originally posted by rnaseek View Post
    samtools manual says they are " ’>’ or ’<’ for a reference skip".

    http://samtools.sourceforge.net/samtools.shtml
    Thank u! This is really helpful!

    Leave a comment:


  • rnaseek
    replied
    samtools manual says they are " ’>’ or ’<’ for a reference skip".

    Leave a comment:


  • hanleng
    started a topic mpileup format

    mpileup format

    I am using samtools mpileup to analyze my data, and have several lines like this:

    chr1 14976 G 5 <<><> HHHHH
    chr1 14977 C 5 <<><> HHHHH
    chr1 14978 C 5 <<><> HHHHH
    chr1 14979 T 5 <<><> HHHHH
    chr1 14980 C 5 <<><> HHHHH
    chr1 14981 A 5 <<><> HHHHH
    chr1 14982 T 5 <<><> HHHHH
    chr1 14983 G 5 <<><> HHHHH
    chr1 14984 A 5 <<><> HHHHH


    What are those ">" "<" or "*" mean in the reads base column? According to the description of the format (http://samtools.sourceforge.net/pileup.shtml), they should be only in the base qualities columns.

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