I found some minor errors in the naming of the --include-introns flag that was causing errors with writing output files. Additionally, I have altered the workflow slightly to make it easier to alter when we want to automate it to use the --include-introns flag for all snRNA-seq samples.
To now implement the --include-introns flag in cellranger count, you should be able to use the flag --premrna at the command line.
I found some minor errors in the naming of the
--include-intronsflag that was causing errors with writing output files. Additionally, I have altered the workflow slightly to make it easier to alter when we want to automate it to use the--include-intronsflag for all snRNA-seq samples.To now implement the
--include-intronsflag in cellranger count, you should be able to use the flag--premrnaat the command line.