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  • pileup file symbols "<" and ">"

    Hi all,

    I have some problems with my pileup file. I used Tophat to map my RNA-seq reads and samtools mpileup to generate my output file. An example of the first 5 columns (without the column for base qualities) is as follows:

    chr1 155743 N 15 <<<>>><>>>>><Gg
    chr1 155744 N 15 <<<>>><>>>>><Tt
    chr1 155745 N 15 <<<>>><>>>>><Aa
    chr1 155746 N 15 <<<>>><>>>>><Cc
    chr1 155747 N 15 <<cCCCcCCCCCcCc
    chr1 155748 N 15 <<tTTTtTTTTTtTt
    chr1 155749 N 15 <<gGGGgGGGGGgGg
    chr1 155750 N 15 <<aAAAaAAAAAaAa

    It's showing N because I did not use a reference index. However, my question is why there are < and > in the column for read bases? I'm thinking they might refer to reads that span exon-exon junctions. Has anyone else encountered them before?

    Thanks.

  • #2
    Yes, those are places which are between exon junctions (intronic sequence). The specification document could use this to be added.

    Comment


    • #3
      Thank you! I thought so from comparing different positions, but was not sure.

      Comment


      • #4
        Can you identify read bases from these sequences?

        Hello,
        I have a similar pileup file, and I am trying to calculate information content at each position in the alignment. Is it possible to tell from the '<' and '>' characters what the specific read bases are? Sorry if I've missed something completely obvious and thanks for your help.

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