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  • tag density distribution over the gene body

    Dear All,

    I have a bam file of a MeDIP seq sample.
    I have also a bed file of all mouse genes.

    I would like to plot the tag density over the genebody as illustrated in this two examples I found in the literature.

    I know how to plot the tag density distribution relative to the TSS and +2kb/-2kb both, but how do I deal with the gene body?

    Many Thanks,
    Paolo
    Attached Files

  • #2
    try ngsplot

    Quick mining and visualization of NGS data by integrating genomic databases - shenlab-sinai/ngsplot

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    • #3
      Honestly I would like to avoid installing Galaxy in my server, any other suggestion?

      Comment


      • #4
        Hi Paolo,

        have you tried Ensembl's Perl API in combination with the Bioperl's Samtools?
        A nice tutorial can be found here.

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        • #5
          Originally posted by paolo.kunder View Post
          Honestly I would like to avoid installing Galaxy in my server, any other suggestion?
          I don't think you need to install Galaxy.

          Code:
           A user only needs to write a very small configuration file, telling the program which samples to look at and how they should be combined with different regions, and then run the program with one command line. A web-based version (Galaxy) of ngs.plot is also developed to be used by wet-lab biologists who tend to be averse to command line usage.

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          • #6
            I think you need to install it,
            anyway some other suggestions?

            Comment


            • #7
              No, you don't need Galaxy. What harryzs posted (directly from the ngsplot website) is correct.

              I'm using ngsplot and I do not have Galaxy installed on my server.

              Comment

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