Updates the Fastq generation pipeline and the make_fastqs command to add a new --rc-i2-override option for the 10x_visium protocol (which handles 10x Genomics Visium spatial RNA-seq data). This in turn is used to set the eponymous option in the spaceranger mkfastq command, to explicitly specify the workflow used to prepare the samples (and thus map the 10x Genomics indexes to the correct sequences for demultiplexing).
Spaceranger should automatically determine the workflow however the switch can be used to override this and explicitly specify which to use:
--rc-i2-override=false: use for workflow A (older forward strand workflow)
--rc-i2-override=true: use for workflow B (current reverse complement workflow)
Updates the Fastq generation pipeline and the
make_fastqscommand to add a new--rc-i2-overrideoption for the10x_visiumprotocol (which handles 10x Genomics Visium spatial RNA-seq data). This in turn is used to set the eponymous option in thespaceranger mkfastqcommand, to explicitly specify the workflow used to prepare the samples (and thus map the 10x Genomics indexes to the correct sequences for demultiplexing).Spaceranger should automatically determine the workflow however the switch can be used to override this and explicitly specify which to use:
--rc-i2-override=false: use for workflow A (older forward strand workflow)--rc-i2-override=true: use for workflow B (current reverse complement workflow)More information can be found in the 10x knowledge base article at https://kb.10xgenomics.com/hc/en-us/articles/360056364852-Should-I-select-Workflow-A-or-Workflow-B-for-the-i5-index-sequence-
NB testing with Spaceranger 1.3.1 suggests that the effect of the
true/falsesettings might be the opposite of those above?