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griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
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cannot detect strandedness from cellranger bam file #173

Closed ckong1806 closed 1 year ago

ckong1806 commented 1 year ago

Hi, I have 10X genomics 3' scRNAseq data that I've processed through cellranger. I have the possorted bam output file and I am trying to run regtools to obtain the splice junctions bed file. Since cellranger uses STAR alignment, there is no info on strand specificity - how do I go about this?

SebastianMHJohn commented 1 year ago

Hi, I have the same issue. I would greatly appreciated any suggestions. Best wishes

kcotto commented 1 year ago

We have an option that you can use -C that will use information in the fasta file to try to assign strandedness to reads. More information here: https://regtools.readthedocs.io/en/latest/commands/cis-splice-effects-identify/

SebastianMHJohn commented 1 year ago

Thanks for your quick response