rmats

HudsonAlpha · Dec 2, 2016 · c752030 · c752030
1 parent 801dace
commit c752030
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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