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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

Argument Description
${path_to_ciscall.py} Path to cisCton/ciscall.py
-a ${analysis_type} See cisCton analysis type
-d ${data_directory} cisCton data directory, in which you need to store input files other than ciscall.config and .bam files generated in a cisMuton run.
-w ${working_directory} cisCton working directory, in which you need to put the tmp/ directory (.bam files are under it) generated by cisMuton before running cisCton. cisCton generates output files under this working directory.
-m ${path_to_samtools} Path to the samtools command, preferably cisFusion/bin/samtools or cisMuton/bin/samtools
-b ${path_to_bigWigToBedGraph} Path to the cisCton/utility/bigWigToBedGraph command
${SAMPLE_NAME} Target (foreground) sample name. This should be the same name as for cisMuton.
${BG_SAMPLE_NAME} Control (background) sample name. This should be the same name as for cisMuton.
-p ${GROUP} Group name. Only ${GROUP} should be set in this argument. ${GROUP}.bed should be in the directory specified by -d.
-r ${reference_fasta_file} Reference fasta file name without the path. This file should be in the directory specified by -d.
-g ${refGene_file} refGene file name without the path. This file should be in the directory specified by -d.
[ -n ${thread_num} ] Maximum number of threads. If this is not specified or if a value greater than the number of available CPU cores is specified, then the number of maximally available CPU cores is set instead.
-l debug Debugging option

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.

cisCton Analysis Type Target Sample Control (Background) Sample Description
CTON:DUP FFPE frozen/cell-line DUP is an argument to remove duplicates (recommended for FFPE samples)

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 Name Description
${SAMPLE_NAME}.${GROUP}/Cton/ CNA call directory
${SAMPLE_NAME}.${GROUP}/Cton/bed.cnv_target_dup.txt* CNA calls for target bed regions
${SAMPLE_NAME}.${GROUP}/Cton/gene.cnv_target_dup.txt* CNA calls for genes
${SAMPLE_NAME}.${GROUP}/Cton/${SAMPLE_NAME}_target_dup.exonlrr.pdf* Log R ratio graph of exon regions
${SAMPLE_NAME}.${GROUP}/supplement/ Other supplementary information
${SAMPLE_NAME}.${GROUP}/Param/ Version, settings and parameters
  • * 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.
Column Description
Bed.Chr Chromosome
Bed.Stt Start position (1-based)
Bed.End End position (1-based)
Segment.Id CNA segment ID
Segment.Call Neutral/Amplification/Deletion
Segment.Call.PValue p-value for segment calling
Segment.Call.EffectSize Effect size for segment calling
Segment.Median_LogR Median log R ratio of the segment
Gene Gene
LogRatio Log R ratio of this bed region
CrctDepthFG.Val GC-corrected depth in this bed region for the sample
CrctDepthBG.Val GC-corrected depth in this bed region for the control
RawDepthFG.Val Raw depth in this bed region for the sample
RawDepthFG.Avg Raw depth averaged across all bed regions for the sample
RawDepthBG.Val Same as FG
RawDepthBG.Avg Same as FG
Mappabil_Uniq 1 if the mappability is one in this bed region; otherwise, 0.

(2) gene.cnv_target_dup.txt

  • CNA calls for genes.
  • Only amplifications are detected for the reasons described in the accompanying paper.
Column Description
Chr Chromosome
Gene Gene
Gene.Call Amplified/NotAmplified
Gene.LogR Log R ratio of the gene
SegAmp.LogR Log R ratio of amplified segments included in the gene
SegNeu.LogR Log R ratio of neutral segments included in the gene
SegDel.LogR Log R ratio of deleted segments included in the gene
SegAmp.Coverage Coverage of amplified segments over the gene
SegNeu.Coverage Coverage of neutral segments over the gene
SegDel.Coverage Coverage of deleted segments over the gene

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


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