diff --git a/lib/config.py b/lib/config.py index a69ffb8..eeca08b 100644 --- a/lib/config.py +++ b/lib/config.py @@ -32,7 +32,7 @@ # referenced STAR arguments within the corresponding dictionary values star_options = {"default": "", "encode": "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000", - "fusion": "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 200000 --alignMatesGapMax 200000"} + "fusion": "--alignSJDBoverhangMin 10 --chimJunctionOverhangMin 12 --outReadsUnmapped None --chimSegmentMin 12 --alignMatesGapMax 200000 --alignIntronMax 200000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5"} # ENVIRONMENT VARIABLES: # The following system environment variables are changed to add or overwrite