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:

• * ${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