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  • BBMap pileup questions

    I am interested in metrics that summarise coverage from my BAM file. I came across BBMap pileup which does a decent job. But I have a couple of questions.

    1. It seems like if a window is provided to pileup, it returns the sum over the given window. Can other metrics such as sum/mean/median/min/max/sd/mad be calculated? I am particularly interested in the median.

    2. Does pileup do only fixed windows or can it do sliding window metrics?

    3. BBMap pileup returns a summary over the whole file to the console like below:

    Average coverage: 71.19
    Standard deviation: 198.58
    Percent scaffolds with any coverage: 100.00
    Percent of reference bases covered: 97.66

    Can this be saved to a file? I tried '> summary.txt' at the end of my script but that didn't work.

    Thanks,
    Roy

  • #2
    Have you tried using "out=" to save the results to a file.

    Comment


    • #3
      Hallo,

      I assembled metagenomic reads and want to know how many reads are mapping to the contigs.

      I created a sam file using bbwrap for paired-end libraries with singletons. So the sam files consist of paired and unpared reads.

      The log file of bbwrap shows me that for different samples reads are mapped usually 40-70% of the paired and 30-50% of the singeltons. However, the pileup log files say that in all samples 48-49% of reads were mapped. This makes no sense to me.

      I used v 37.78 and activated physical coverage.
      Can pileup not handle paired end + singletons in the same file?


      Edit:
      it seems that it's due to the physical cov.
      Last edited by silask; 06-04-2018, 12:18 AM.

      Comment


      • #4
        There is still something strange.

        in the log file of bbwrap I have


        Code:
        * | Paired end | Se
        -- | -- | --
        Total reads | 2 x 16895000 | 31401969
        mapped | 2x 13408609 | 29907540
        * | * | *
        mapped | 79% | 95%
        Which seem to be correct. e.g. the number of unmapped reads are found in `outu`


        in the logfile of pilup it is written:
        Code:
        Reads: | 27370533
        -- | --
        Mapped reads: | 26817218
        Mapped bases: | 4022582700
        Ref scaffolds: | 851270
        Ref bases: | 1216084673
        * | *
        Percent mapped: | 97.978
        Percent proper pairs: | 97.978
        I have no Idea, how pilup finds only 27370533 reads.
        Last edited by GenoMax; 06-06-2018, 04:34 AM.

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