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Add link to strandedness table
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kcotto committed May 6, 2021
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2 changes: 1 addition & 1 deletion docs/commands/cis-splice-effects-identify.md
Expand Up @@ -22,7 +22,7 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
| -o STR | Output file containing the aberrant splice junctions with annotations. [STDOUT] |
| -v STR | Output file containing variants annotated as splice relevant (VCF format). |
| -j STR | Output file containing the aberrant junctions in BED12 format. |
| -s INT | Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. |
| -s INT | Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. If you are unsure, we have created this [table](https://rnabio.org/module-09-appendix/0009/12/01/StrandSettings/) to help. |
| -w INT | Window size in b.p to identify splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons. |
| -e INT | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3] |
| -i INT | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2] |
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