10X 5' single-cell data

[HenriettaHolze]

Hi @hxj5 , I have a question regarding 10X 5' scRNA-seq data.
For 5' sequencing, the read containing cell barcode and UMI contains part of the transcript https://kb.10xgenomics.com/hc/en-us/articles/360000939852-What-is-the-difference-between-Single-Cell-3-and-5-Gene-Expression-libraries.
The 10X CellRanger pipeline therefore includes both the forward and reverse read in the BAM file.
You mention in #121 that only one read per cell barcode UMI combination is used to extract the allele. In that case, only either the forward or reverse read is considered and almost half the data is discarded. Is this correct?

Cheers, Henrietta