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cisFusion

cisFusion is a caller that detects fusion genes. cisFusion is run in the same fashion as cisMuton.

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

1. Running cisFusion

1.1. Basic Steps

The basic steps to run cisFusion are as follows.

  1. Prepare all prerequisite files under the execution directory and set the parameters.
    For these inputs, see the Inputs section and the cisCall Installation section for further details.

  2. Run cisFusion in the execution directory.

     $ cd /path_to_execute/
     $ perl /path_to_cisFusion_install_directory/qc_run.pl ${SAMPLE_NAME}:${BG_SAMPLE_NAME}:${GROUP}:FUSION,${CAPTURE_REGION},${OPTION},${CAPTURE_SIDE}
    						

1.2. cisFusion Arguments

${CAPTURE_REGION} and ${CAPTURE_SIDE} must be either of the following two combinations (other combinations are not allowed):

  • TARGET,BOTHSIDES: to find fusion gene pairs, both of which are listed in ${GROUP}.fusion.bed.
  • WEXOME,ONESIDE: to find fusion gene pairs, either of which are listed in ${GROUP}.fusion.bed.

In the case of an FFPE target (foreground) sample, set FFPE to the head of ${OPTION}.

In addition to the FFPE option, we recommend the following options for FFPE samples to remove duplicates. Set these as follows.

  • For an FFPE target (foreground) sample: set DUP to ${OPTION}.
  • For an FFPE control (background) sample: set DUP_BG to ${OPTION}.

The following command illustrates the case of target-captured FFPE target samples and FFPE control samples:

$ perl /path_to_cisFusion_install_directory/qc_run.pl ${SAMPLE_NAME}:${BG_SAMPLE_NAME}:${GROUP}:FUSION,TARGET,FFPE,DUP,DUP_BG,BOTHSIDES
					

See the Miscellaneous Options section for details on removing duplicate sequence reads.

1.3. Removing Adapter Sequences

Adapter sequences can be removed using cisCall. See the Miscellaneous Options section for details.

2. cisFusion Output

Running cisFusion will create the following directories and a log file in the execution directory:

  • output/: outputs
  • tmp/: temporary files
  • log.txt: log file

In the case of running cisFusion in the same execution directory after a preceding run, remove the tmp directory beforehand. Semaphore lock files with .lock cause abnormal program termination.

2.1. Contents of the output/ Directory

Running cisFusion creates the following output files in the execution directory:

File Name Description
output/Call.${SAMPLE_NAME}-RA.${GROUP}/Fusion/Call.${BG_SAMPLE_NAME}-RA/ A directory containing the following output file
Aln${mode}_${side}_Mq*_Paired.txt A call table assuming paired-end reads*, **
Aln${mode}_${side}_Mq*_Single.txt A call table assuming single-end reads*, **
  • * ${mode} will be named as either Target or Wexome according to the cisFusion arguments:
    • In case of TARGET and BOTHSIDES, it will be named as Target
    • In case of WEXOME and ONESIDE, it will be named as Wexome
  • ** ${side} will be named as either LmtOneside or Lmtbtheside according to the cisFusion arguments:
    • In case of TARGET and BOTHSIDES, it will be named as Lmtbtheside
    • In case of WEXOME and ONESIDE, it will be named as LmtOneside

You can see examples of the output files (https://bioinfoncc-my.sharepoint.com/personal/bioinfo_bioinfoncc_onmicrosoft_com/_layouts/15/guestaccess.aspx?docid=0beb536690e86454d9cd6cc8fa935b82d&authkey=AQdUocTX6-YuuVTcsnnT41s) generated by cisFusion for the short example of test data.

2.2. Output Format of the Call Table

Column Description
Pair Names of fusion gene candidates
Call Whether call criteria are satisfied. See only rows with 1 as calls.
Nrmcnt_total Total support read count normalized by mapped read count
Nrmcnt_2map Support read count detected at the 2map step normalized by mapped read count
Nrmcnt_2map+paired Support read count detected at the 2map and paired-end steps normalized by mapped read count (only for *_Paired.txt)
2map_count Support read count detected only at the 2map step
2map&VF_count ("Common_count" in *_Single.txt) Support read count detected at both the 2map and VF steps
VF_count Support read count detected only at the VF step
Paired_count Support read count detected (only) at the paired-end step (only for *_Paired.txt)
OnlyVF_Prop(OnlyVF/Total) Ratio of the noted support reads
OnlyVF_Prop(OnlyVF/2map) Ratio of the noted support reads
OnlyVF_Prop(OnlyVF/(2map+paired)) Ratio of the noted support reads (only for *_Paired.txt)
MapCount_Pval P-value in Fisher's exact test when reads from control (background) data are available
GeneDepth:BiasG1G2 Index used to measure a bias based on depth of Gene1 / total depth of Gene1 + Gene2
GeneDepth:TotalG1G2 Total depth of Gene1 + Gene2
Gene1 Name of Gene1
Gene1:Breakpoint Breakpoint of Gene1
Gene1:Nrmcnt Normalized count of support read candidates
Gene1:Count Count of support read candidates
Gene1:Count_SN Index used to measure signal-to-noise using support read candidate count
Gene1:GeneDepth Depth of Gene1
Gene2 Same as Gene1
Gene2:Breakpoint Same as Gene1
Gene2:Nrmcnt Same as Gene1
Gene2:Count Same as Gene1
Gene2:Count_SN Same as Gene1
Gene2:GeneDepth Same as Gene1

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