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  • How to plot each ChIPseq peak ??

    Dear all,
    I have ChIP-seq data now and trying to make plot for each peak. I have .bam file and peak regions. how can I make coverage plot (RPKM) for each peak?

    For example, I have a peak covers genome from 1kb to 1.5kb, so what I want is a line plot shows the reads coverage over the region, Y axis is RPKM and X axis is genome region from 1 to 1.5 kb, like draft in attached picture. preferably, I will plot IP sample with negative control together.

    I didn't find good program to do this, so if you know any program, or you have any suggestion, please tell me. Thank you very much!

    Best,

    /Kun
    Attached Files

  • #2
    I think what you want is mostly the coverage of each bp of your genome (then you have to use RPM if you want to normalize different samples).

    I would use genomeCoveragedBed to generate bedgraphs. Then, with awk you can easily normalize the values considering the number of mapped reads...

    Afterwards, either you load the resulting files in a genome browser like igv, or you can generate yourself the pictures of your regions of interest (I personnally use R for this).

    Good thing with genomeCoveragedBed is you can make pictures showing the coevarge of each strand (-strand option).

    s.

    Comment


    • #3
      Thank you, SylvainL. It is what I want to have.
      I will start with genomeCoveragedBed, but I am not very familiar with R, is there any tools in R package can do plot?

      Comment


      • #4
        Originally posted by babykooo View Post
        Dear all,
        I have ChIP-seq data now and trying to make plot for each peak. I have .bam file and peak regions. how can I make coverage plot (RPKM) for each peak?
        I wrote a program for that, which I mentioned here http://seqanswers.com/forums/showthr...965#post160965. See if it helps... The minimal syntax is

        Code:
        genomeGraphs -b peaks.bed -i aln_1.bam aln_2.bam aln_n.bam --rpm
        And for each interval in peaks.bed you get a profile figure in pdf format.

        Comment


        • #5
          Hi dariober, I still like to have a line graph, but I will try your program also, thank you!.

          Comment


          • #6
            Originally posted by babykooo View Post
            Hi dariober, I still like to have a line graph, but I will try your program also, thank you!.
            Hi- if you just want to have lines you can avoid filling in the area under the coverage profile with '--col_track NA --col_track_rev NA'. To have the line of a colour of your choice use "--col_line". Like:

            Code:
            genomeGraphs -i aln1.bam aln2.bam -b mypeaks.bed --col_track NA --col_track_rev NA --col_line red
            Also, if you set '--tmpdir mytmpdir' the files used for plotting will be saved into "mytmpdir" so you can use your scripts to plot them.

            (By the way I moved genomeGraphs here https://github.com/dariober/genomeGraphs)

            Comment


            • #7
              Originally posted by dariober View Post
              I wrote a program for that, which I mentioned here http://seqanswers.com/forums/showthr...965#post160965. See if it helps... The minimal syntax is

              Code:
              genomeGraphs -b peaks.bed -i aln_1.bam aln_2.bam aln_n.bam --rpm
              And for each interval in peaks.bed you get a profile figure in pdf format.
              Hi Dariober, I tried you code, but got error message, you can see the attached message. I didn't use -o option. any suggestion for me?
              Attached Files

              Comment


              • #8
                Originally posted by babykooo View Post
                Hi Dariober, I tried you code, but got error message, you can see the attached message. I didn't use -o option. any suggestion for me?
                Hi- I think the issue is that your default shell appears to be sh, which doesn't support "set -o pipefail" (this is part of the commands internally executed). I changed the code to make python explicitly use bash instead of sh.

                Would you mind re-downloading the package from https://github.com/dariober/genomeGraphs and reinstall it?

                Keep me posted if you get into troubles... I'll try to help!

                Dario

                Comment


                • #9
                  Originally posted by dariober View Post
                  Hi- I think the issue is that your default shell appears to be sh, which doesn't support "set -o pipefail" (this is part of the commands internally executed). I changed the code to make python explicitly use bash instead of sh.

                  Would you mind re-downloading the package from https://github.com/dariober/genomeGraphs and reinstall it?

                  Keep me posted if you get into troubles... I'll try to help!

                  Dario
                  Hi Dario
                  It works this time! Now I can try to change some parameters to plot. Thank you very much!

                  /Kun

                  Comment


                  • #10
                    Originally posted by babykooo View Post
                    Hi Dario
                    It works this time! Now I can try to change some parameters to plot. Thank you very much!

                    /Kun

                    Cool thanks for letting me know. If you want to play with the graphic parameters I would suggest you plot just one or few bed intervals to start with. So you don't have to wait too long for the program to finish. E.g., plot only first two peaks:

                    Code:
                    head -n 2 fileWithManyPeaks.bed \
                    | genomeGraphs -b - -i aln_1.bam

                    Comment

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