Single-Cell Quantification from BAM File with CB and UB Tags

[dawangran]

Hello,
I am working on single-cell RNA-seq data analysis and I have a BAM file where the reads start from the polyT position. The BAM file contains tags for cell barcodes (CB) and unique molecular identifiers (UB). Additionally, I have a barcode_beads.tsv file that lists the CB and UB information for each read.
I am looking to perform quantification using this data. Could you please provide guidance on the best approach to achieve this? Specifically, I am interested in understanding the following:
How to extract the CB and UB information from the BAM file for further analysis.
How to use the barcode_beads.tsv file in conjunction with the BAM file for accurate quantification.
Any recommended tools or pipelines that can handle this type of data efficiently.
Any insights or suggestions would be greatly appreciated.
Thank you for your help.
Best regards,
Dawn

[andrewprzh]

Dear @dawangran

Yes, you can perfectly use Spl-IsoQuant with this data!
You need to input your provide you bam file via --bam option and barcode_beads.tsv via --barcoded_reads. It should contain read id, barcode and UMI sequences.

You can also provide a BAM file and a whiltelist of barcodes and use Spl-IsoQuant barcode detection depending if it supports the technology you used.

Best
Andrey