You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/commands/junctions-extract.md
+1-1Lines changed: 1 addition & 1 deletion
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -18,7 +18,7 @@ The `junctions extract` command can be used to extract exon-exon junctions from
18
18
| -o | File to write output to. STDOUT by default.|
19
19
| -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.|
20
20
| -h | Display help message for this command.|
21
-
| -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.
21
+
| -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.
22
22
23
23
###Output
24
24
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.
0 commit comments