Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
dewyman authored Sep 25, 2019
1 parent 95b6fc3 commit 51c6e0b
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +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.
| --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 and Fasta files at the end of the run.

### Other options that may help tune performance
| Option | Shortcut | Description
Expand Down

0 comments on commit 51c6e0b

Please sign in to comment.