Reads per UMI from 10X Chromium RNAseq runs

Question

[Raghuvanshi Rajesh]

I am working on a set of Drosophila samples sequenced using 10X Chromium pipeline and I need to visualize the reads of individual cells on IGV.

Unlike SMARTseq methods which yield an individual BAM file for each UMI, CellRanger outputs only a bulk RNAseq-like BAM for the entire sequencing. Is there a method by which I could take the output BAM files from CellRanger and subset the reads of specific UMIs (to remove reads from low quality, doublet and apoptotic cells) rather than the entire sequencing run?

Answer 1

[swbarnes2]

Are you sure you want UMIs, and not cell barcodes?

Anyway, the bams have useful tags which you could use for filtering

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam