From 95b6fc3de556de707950c0cde85db776ebfa31db Mon Sep 17 00:00:00 2001 From: Dana Wyman Date: Wed, 25 Sep 2019 15:20:31 -0700 Subject: [PATCH] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index eddc60f..eecc073 100644 --- a/README.md +++ b/README.md @@ -41,6 +41,7 @@ TranscriptClean is run from the command line as follows. Please note that releas | --maxLenIndel | n/a | Maximum size indel to correct. Default = 5 bp. | --maxSJOffset | n/a | Maximum distance from annotated splice junction to correct. Default = 5 bp. | --primaryOnly | n/a | If this option is set, TranscriptClean will only output primary mappings of transcripts (ie it will filter out unmapped and multimapped lines from the SAM input.) +| --canonOnly | n/a | If this option is set, TranscriptClean will only output transcripts that are either canonical or that contain annotated noncanonical junctions to the clean SAM file at the end of the run. ### Other options that may help tune performance | Option | Shortcut | Description