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.
rnabioco · Feb 15, 2024 · b131023 · b131023
1 parent 1f0356f
commit b131023
Showing 1 changed file with 2 additions and 0 deletions.
diff --git 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 \