From 8921cb6b0cc72d9bb34a3d16870e583eade97cc5 Mon Sep 17 00:00:00 2001 From: Felix Krueger Date: Tue, 3 Sep 2024 13:56:49 +0100 Subject: [PATCH] added --strandID to docs --- docs/options/alignment.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/options/alignment.md b/docs/options/alignment.md index 90759be..99b91ac 100644 --- a/docs/options/alignment.md +++ b/docs/options/alignment.md @@ -132,6 +132,10 @@ In this mode, it is not required that the entire read aligns from one end to the Sets the SM field in the `@RG` header line; can't be set without setting `--rg_id` as well. Default: SAMPLE +- `--strandID` + +For non-directional paired-end libraries, the strands identity is encoded by the order in which R1 and R2 are reported, as well as the read and genome conversion state. If third party tools re-organise this order it may become difficult to determine the alignment strand identity. This option adds an optional tag, e.g. `YS:Z:OT` or `YS:Z:CTOB` to preserve this information. See also [this thread for more details](https://github.com/FelixKrueger/Bismark/issues/455). Default: OFF. + - `--quiet` Print nothing besides alignments.