How to Analyze 10x Genomics Data with Full-Length R1 and R2 (100bp Each)?

Question

[zbidav]

Dear Biostars community,

I’m used to analyzing 10x Genomics single-cell RNA-seq data where R1 is typically 26bp (cell barcode + UMI) and R2 is longer (~100bp, cDNA read). However, I’ve encountered a dataset (GSM6782325) where both R1 and R2 are 100bp long, which is unusual (at least for me) for standard 10x data.

Link to SRA sample

From what I understand, the R1 contains full sequencing of the polyA. I’m however, unsure how to analyze this type of sequencing data properly. Is this still valid 10x data? Does Cell Ranger support processing this, or do I need custom preprocessing?

Thanks in advance!

Answer 1

[GenoMax]

Cell ranger should be able take what it needs from read 1. Proceed as normal.