issues with generating splice junction file

[ckong1806]

I have 3' scRNAseq data from 10X genomics. I ran the data through cellranger so, I have the possorted bam ouput file. I tried to run regtools on the bam file but, the bed output file has ? in the strand column. Regtools wasn't able to detect strandedness since cellranger used STAR for alignment and STAR doesn't infer strandedness. From the vignette in Sierra, it seems you guys also used cellranger output - can you share how were you able to run regtools on your dataset?