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  • Making a bedGraph from a Bowtie file

    Hi everyone,

    I have a few Bowtie alignment files that I would like to view unsmoothed (I usually use Fseq to find peaks and it smoothes things over) to get an idea of read depth. Is there any way to convert a Bowtie output file to a bedGraph?

    Thanks!

  • #2
    Originally posted by gez View Post
    Hi everyone,

    I have a few Bowtie alignment files that I would like to view unsmoothed (I usually use Fseq to find peaks and it smoothes things over) to get an idea of read depth. Is there any way to convert a Bowtie output file to a bedGraph?

    Thanks!
    If you use sam output from Bowtie, you could use the genomeCoverageBed tool from my BEDTools package as follows:

    Code:
    samtools view -Sb bowtieOut.sam | genomeCoverageBed -ibam stdin -g <genomefile> -bg > out.bedgraph
    Note that the <genomefile> is a special file in BEDTools denoting the lengths of each chromosome. The "chromInfo" files from UCSC can be used.

    Best,
    Aaron

    Comment


    • #3
      Hi,

      genomeCoverageBed requires a sorted bowtieOut.sam
      the following code worked for me:

      Code:
      samtools view -Sbo bowtieOut.bam bowtieOut.sam # convert to bam format
      samtools sort bowtieOut.bam sortedbowtieOut.bam # sort the bam file
      genomeCoverageBed -bg -ibam sortedbowtieOut.bam -g chrominfo.txt > out.bedgraph # compute coverage
      see http://groups.google.com/group/bedto...usage-examples

      -Lionel

      Comment

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