From b13102359a4dc47f662f31655463d27dbacececa Mon Sep 17 00:00:00 2001
From: Austin Gillen <4809242+agillen@users.noreply.github.com>
Date: Wed, 14 Feb 2024 23:29:35 -0700
Subject: [PATCH] Fix strand assignment for R1 and paired alignment rules

Change results in correct gene assignment (GX/GN tags) by STARsolo but does not impact featureCounts of bed generation downstream.
---
 rules/cutadapt_star.snake | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/rules/cutadapt_star.snake b/rules/cutadapt_star.snake
index cfaecb4..e51f10f 100644
--- a/rules/cutadapt_star.snake
+++ b/rules/cutadapt_star.snake
@@ -155,6 +155,7 @@ rule starsolo_R1:
       --runThreadN 12 \
       --soloCBwhitelist {params.chemistry} \
       --soloBarcodeMate 1 \
+      --soloStrand Reverse \
       --outFilterMultimapNmax 1 \
       --outFilterMismatchNmax 999 \
       --outFilterMismatchNoverReadLmax 0.2 \
@@ -241,6 +242,7 @@ rule starsolo_paired:
       --soloCBwhitelist {params.chemistry} \
       {params.star_args_paired} \
       --soloBarcodeMate 1 \
+      --soloStrand Reverse \
       --outFilterMultimapNmax 1 \
       --outFilterMismatchNmax 999 \
       --outFilterMismatchNoverReadLmax 0.2 \