CTCF_orientation

CTCF_orientation is a python tool that produces a pie chart visualizing the CTCF orientation of chromatin loops in a given loop file.

Requirements

• python 3.7
• pandas
• matplotlib

Usage

ctcf_orientation.py -l <loopfile> -m <motiffile> -o <outputfile>

Parameters

• -l; loop file: chromatin loop file in bedpe format (see bedtools documentation for more information), with or without a header row.
• -m; motif file: CTCF motif file in the format "chromosome start end motif score strand p.value q.value sequence", although only the chromosome, start, end, and strand columns will be used. The one provided as an example is for the hg19 genome assembly.
• -o; output file: Filepath to outputted piechart in any matplotlib accepted format (see matplotlib picture formats for more information)
• -h; help: Helpful information for usage.

Output

CTCF_orientation produces a pie chart showing the distribution of CTCF motifs in the chromatin loop dataset provided. CTCF motifs will be binned into 5 categories: convergent, divergent, tandem, single, and none depending on which CTCF motifs the first anchor of the loop intersects with and which the second does. For example, if the first anchor contains a CTCF site but the second doesn't, that loop is designated as containing a 'single' CTCF site. If both anchors contain CTCF sites on the same strand, the loop contains a tandem CTCF motif, etc.

Example

ctcf_orientation.py -l ./test_data/data/grubert_hg19_gm12878_original_loops.bed -m ./test_data/CTCF.bed -o ./test_data/gm12878_hg19_grubert_loops_ctcf_piechart.svg

Thanks

• CTCF, Source for CTCF motif files and ideas.