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  • conversion tool sam to wig

    Does anyone have a conversion tool for .sam format to .wig format? I need to visualize my aligment data on ucsc.
    Thanks!!

  • #2
    In Unix/Linux, a one-liner could do this for you:

    samtools pileup -S -f <reference fasta> <sam file> | awk '{print $1, $2-1, $2, $4}' > mywiggle.bed

    --Nancy

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    • #3
      Nice! BTW it creates a huge wig file as it gives a value for each position.
      I would post-process the data with some binning tool (such as wig2bdg included in MACS). As example:
      bam file with ~12000000 aligned reads -> 1.7 Gb compressed wig -> 87 Mb compressed binned bedgraph

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      • #4
        nhansen:
        I follow your methods and samtools show "[bam_plp_destroy] memory leak: 1. Continue anyway."
        Dose it mean I don`t have enough memory?

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