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  • How to convert sam/bam or bed file into wig file

    Hi,

    How what tools can I use to convert sam/bam or bed file into a wig file?

  • #2
    There are several options. I use bedtools genomeCoverageBed to convert from BAM to BedGraph. Then bedGraphToBigWig to convert BedGraph to BigWig.

    Maybe someone else knows of a single step option.

    Comment


    • #3
      I wrote a Bam2wig : https://github.com/lindenb/jvarkit/wiki/Bam2Wig
      It use the cigar elements to get the depth.

      ( however, I did not often used it)

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      • #4
        if this is RNA-seq data, be sure to use the -splice option for genomeCoverageBed

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        • #5
          Originally posted by id0 View Post
          There are several options. I use bedtools genomeCoverageBed to convert from BAM to BedGraph. Then bedGraphToBigWig to convert BedGraph to BigWig.

          Maybe someone else knows of a single step option.
          This is chip-seq data and i used the following commands

          1. bedtools genomecov -bg -ibam Mysorted.bam > Mysorted.bedGraph

          2. bedgraphToBigWig in.bedGraph chrom.sizes out.bw

          At step 2, I am not sure if I understand what is the chrom.sizes file is. Shall i just create one myself simply subtracting end position from the start position to create the chrom.sizes?
          I guess 'in.bedGraph' is my Mysorted.bedGraph.

          Am i missing something?

          Comment


          • #6
            When i do the above, i tried to upload it to UCSC genome browser as custom track but it says it cant read my bigwig file.
            I converted my bigwig to wig, this time it gives memory error.

            Any ideas why this might be happening? or how to fix it?

            Comment

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