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  • Tools to plot ChIP-Seq signals in batch

    Hi Guys,
    I wonder if there are tools available for plotting ChIP-Seq signals like attachment (from Tsankov, A. M., et al. (2015). "Transcription factor binding dynamics during human ES cell differentiation." Nature 518(7539): 344-349.). And the plotting could be handled in batch way and result in PDF or SVG. I have tried UCSC and IGV, seems not that convenient.
    Thanks in advance.
    Attached Files
    Last edited by YaqiangCao; 02-24-2015, 11:12 PM. Reason: Add more info

  • #2
    I wrote a program to plot profiles in batch. It's here.

    Say you have bunch of target regions to plot in the bed file regions.bed and for each region you want to see the profile of a number of bam files (or bed or bedgraph):

    Code:
    # Target regions
    cat regions.bed
    chr18	63689	63888
    chr18	158296	158574
    chr18	596941	597204
    chr18	702863	703208
    chr18	712581	712797
    
    genomeGraphs -b regions.bed \
        -i rhh_*.bam regions.bed \
        -s 1000 \
        --col_track_rev NA \
        --col_track blue red \
        --ylab 'Read depth' \
        --ylim max
    Note the use of wild card in "rhh_*.bam" to capture rhh_hacat_05082014.bam rhh_hacat_14062014.bam rhh_hek_09112014.bam rhh_hek_18092014.bam.

    For each interval in regions.bed you get a pdf picture like the one below:



    You should be able to download and install with:

    Code:
    svn checkout http://bioinformatics-misc.googlecode.com/svn/branches/genomeGraphs genomeGraphs
    cd genomeGraphs
    python setup.py install --user --install-scripts $HOME/bin/
    Attached Files
    Last edited by dariober; 03-05-2015, 12:57 AM.

    Comment


    • #3
      Thanks a lot! Any chance for adding gene model in the plot?

      Comment


      • #4
        Originally posted by dariober View Post
        I wrote a program to plot profiles in batch. It's here.

        Say you have bunch of target regions to plot in the bed file regions.bed and for each region you want to see the profile of a number of bam files (or bed or bedgraph):

        Code:
        # Target regions
        cat regions.bed
        chr18	63689	63888
        chr18	158296	158574
        chr18	596941	597204
        chr18	702863	703208
        chr18	712581	712797
        
        genomeGraphs -b regions.bed \
            -i rhh_*.bam regions.bed \
            -s 1000 \
            --col_track_rev NA \
            --col_track blue red \
            --ylab 'Read depth' \
            --ylim max
        Note the use of wild card in "rhh_*.bam" to capture rhh_hacat_05082014.bam rhh_hacat_14062014.bam rhh_hek_09112014.bam rhh_hek_18092014.bam.

        For each interval in regions.bed you get a pdf picture like the one below:



        You should be able to download and install with:

        Code:
        svn checkout http://bioinformatics-misc.googlecode.com/svn/branches/genomeGraphs genomeGraphs
        cd genomeGraphs
        python setup.py install --user --install-scripts $HOME/bin/
        Thanks a lot! Any chance for adding gene model in the plot?

        Comment


        • #5
          Originally posted by YaqiangCao View Post
          Thanks a lot! Any chance for adding gene model in the plot?
          ...Sort of. If you pass a gtf file of gene models it should plot them as bars and lines for exons and introns. Like
          Code:
          genomeGraphs -b regions.bed \
              -i rhh_*.bam regions.bed genes.gtf \
              ...

          Comment

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