Tools to plot ChIP-Seq signals in batch

[YaqiangCao]

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.

[dariober]

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):

# 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:

svn checkout http://bioinformatics-misc.googlecode.com/svn/branches/genomeGraphs genomeGraphs
cd genomeGraphs
python setup.py install --user --install-scripts $HOME/bin/

[YaqiangCao]

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

[YaqiangCao]

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):

# 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:

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?

[dariober]

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

genomeGraphs -b regions.bed \
    -i rhh_*.bam regions.bed genes.gtf \
    ...