cisCton

cisCton is a caller that detects CNAs by comparing target (foreground) and control (background) samples.

Please first read the Quick Start Guide for cisCall for an outline of how to run cisCton.

1. Running cisCton

cisCton requires .bam files generated by running cisMuton. Use the same values for SAMPLE_NAME, BG_SAMPLE_NAME, and GROUP as for cisMuton.

1.1. Basic Steps

The basic steps for running cisCton are as follows.

1. Prepare all prerequisite files under the execution directory.
   For these inputs, see the Inputs section and the cisCall Installation section for further details.
   *Note: Technically, as for cisCton, the "data directory" and "working directory" can be set separately. However, we recommend using the same "execution directory" for both of these in the current version to maintain consistency with cisMuton/cisFusion.

2. Run cisCton in the execution directory.

    $ cd /path_to_execute/
    $ python3 ${path_to_ciscall.py} \
        -a ${analysis_type} \
        -d ${data_directory} \
        -w ${working_directory} \
        -m ${path_to_samtools} \
        -b ${path_to_bigWigToBedGraph} \
        ${SAMPLE_NAME} \
        ${BG_SAMPLE_NAME} \
        -p ${GROUP} \
        -r ${reference_fasta_file} \
        -g ${refGene_file} \
        [ -n ${thread_num} ] \
        -l debug \
        ;
   						

1.2. cisCton Arguments

The following two files must be placed in the data directory specified by -d.

• target_fusion.txt (= ${GROUP}.fusion.bed for cisFusion/cisMuton)
• wgEncodeDukeMapabilityUniqueness20bp.bigWig (included in cisCton)

These two file names must not be changed.

1.3. cisCton Analysis Type

The cisCton analysis type should be set in accordance with the cisMuton settings since cisCton utilizes .bam files generated by cisMuton.

As of the current version, cisCton has been adjusted only to the combination below.

2. cisCton Output

2.1. Contents of the output/ Directory

• cisCton creates the following files in output directory under the working directory specified by the -w argument.
• cisCton generates a log file, called ciscall.log, in the execution directory in addition to output files.

• * File names may be slightly different depending on the settings of cisCton.

You can see examples of the output files (https://bioinfoncc-my.sharepoint.com/personal/bioinfo_bioinfoncc_onmicrosoft_com/_layouts/15/guestaccess.aspx?docid=0b4a6cf7245464277b40d0a9c755c1e7a&authkey=AaGCigH017BQP2cEAAbM37s) generated by cisCton for the short example of test data.

2.2. Output Format of the Call Tables

(1) bed.cnv_target_dup.txt

• CNA calls for target bed regions. Information on CNA segments can be also extracted.
• cisCton uses CNA segment results as the base for gene-based CNA calls in gene.cnv_target.txt.

(2) gene.cnv_target_dup.txt

• CNA calls for genes.
• Only amplifications are detected for the reasons described in the accompanying paper.

Some genes may not be included in this file if they do not satisfy our criteria.