Scripts for the analysis of Tri-C experiments
The TriC_MO.pl script performs the analysis of a Tri-C experiment. It depends on the bam file output of the CCseqBasic pipeline "COMBINED_reported_capture_reads_CS5.bam" (F6 folder), ran using an oligo file without proximity exclusion (see instructions here: http://userweb.molbiol.ox.ac.uk/public/telenius/CCseqBasicManual/), and converted to sam format. This files contains all mapped reads containing 1 capture fragment post PCR duplicate, blat and ploidy filtering. The scripts also requires the oligo file and a file with the coordinates of the restriction fragments (of corresponding enzyme) in the genome.
The script selects the reporter reads in cis, performs a proximity exclusion, maps the reads to the restriction fragments and counts multi-way interactions. These are outputted in a text file with suffix "_TriC_interactions.txt".
Output TriC_MO.pl:
- Report with read and interaction counts
- Text file containing reported multi-way interactions per viewpoint in format: RF1 \t RF2 \t count \n
- Wig file containing all reported interactions in cis per viewpoint (Capture-C like track; optional)
Example of a minimal run command:
nohup perl TriC_MO.pl -sam COMBINED_reported_capture_reads_CS5.sam -o /my_path/tri-c_oligo_file_noprex.txt -r /my_path/mm9_nlaIII_coordinates.txt -name X &
The TriC_matrix_simple_MO.py script plots a simple Tri-C matrix. It depends on the txt file output of the TriC_MO.pl script.
For more details:
python TriC_matrix_simple_MO.py -h
Example of a minimal run command:
python TriC_matrix_simple_MO.py -f /my_path/X_TriC_interactions.txt -l 1 -r 200000 &
For more instructions and more advanced plotting scripts, see http://userweb.molbiol.ox.ac.uk/public/telenius/CCseqBasicManual/