Miscellaneous Options for cisCall

1. Removing Adaptor Sequences

cisCall (cisMuton and cisFusion) can remove adapter sequences from .fastq files, though this may be usually performed using other software such as cutadapt.

To remove adapter sequences using cisCall, use the RMADP command for each of the target (foreground) sample and control (background) sample .fastq files.

$ perl /path_to_install_directory/bin/qc_run.pl ${SAMPLE_NAME}::${GROUP}:RMADP
$ perl /path_to_install_directory/bin/qc_run.pl ${BG_SAMPLE_NAME}::${GROUP}:RMADP
					

This creates .fastq files, with the -RA suffix as output, in which the adapter sequences have been removed. To run cisCall for .fastq files created by this process, add -RA to the ${SAMPLE_NAME}/${BG_SAMPLE_NAME}.

2. Removing Duplicates

Set the following options for ${OPTION} in each command.

• DUP: removes duplicates from the target (foreground) sample .fastq file.
• DUP_BG: removes duplicates from the control (background) sample .fastq file.

To remove duplicates from both the target (foreground) and control (background) samples in cisMuton:

$ perl /path_to_install_directory/bin/qc_run.pl ${SAMPLE_NAME}:${BG_SAMPLE_NAME}:${GROUP}:MUTON,DUP,DUP_BG
					

To remove duplicates from both the target (foreground) and control (background) samples in cisFusion:

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

3. Setting Process/Thread Maximum Values

• To set a maximum number of processes for cisFusion and cisMuton, set the MAX_PROCESS environment variable to your desired number.
• To set a maximum number of threads for cisCton, set -n option. See the cisCton section.