VDJ reconstitution from 3' 10x genomics platforms

Question

[gal.dadi]

Hi All

I have scRNAseq data on B cells from 3' 10x platform.

I want to reconstitute vdj from this data. The only software I found were vdjpuzzle, TRUST4, dandelion and they all works on 5' 10x data.

Are you familiar with one which works on 3' 10x data? If not, what is the reason there aren't softwares that works on 3'?

Thanks

G

Answer 1

[mourisl]

This is because the VDJ region, including CDR3, is located on the 5' of the receptor chain's RNA. The 3'-end of the RNA is the constant gene, which could be more than 1000bp long, and most of the read coverage could not reach the CDR3 region in 3' 10x data.

Nevertheless, you can still get some BCR CDR3 information in 10x 3' data, though the sensitivity would be much lower than 5' data.

[gal.dadi]

Yeah i thought so, are there any platforms that may work on 3'?

I tried cell ranger vdj but i get In the input data, an extremely low rate of correct barcodes was observed for this chemistry (1.4%).

What does it means?

[Ram]

Quick note: Don't use answers unless you're answering the top level question. Use Comments instead. A moderator moved your post this time but please be careful in the future.