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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/junctions-extract.md
Expand Up @@ -18,7 +18,7 @@ The `junctions extract` command can be used to extract exon-exon junctions from
| -o | File to write output to. STDOUT by default.|
| -r | Region to extract junctions in. This is specified in the format "chr:start-end". If not specified, junctions are extracted from the entire BAM file.|
| -h | Display help message for this command.|
| -s | 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 | 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.

###Output
The output is in the BED12 format which is described in detail [here.](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) Each line is an exon-exon junction as explained below.
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