Directly turn bam file to UMI count?

10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

MIT License

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Directly turn bam file to UMI count? #75

Open WT215 opened 2 years ago

WT215 commented 2 years ago

I need to filter out some reads from bam file from visium. Is it possible to directly turn that bam file to UMI count without transforming back to fastq?

I know there are some tools available, but it could not be better if using the same tool as used in space ranger.