BD data

[cathalgking]

@rob-p @robsyme @DongzeHE
I have BD (Becton Dickinson) single-cell RNA-seq data that I want to align. Can I do this with simpleaf?
Thanks

[DongzeHE]

Hi @cathalgking,

I think simpleaf is able to handle most existing protocols. For me to investigate this and provide a solution, would you mind telling me which exact system from BD you are using? It would be great if you could provide some information about their chemistry specification, like (1) where are the UMI and CB located, (2) how many times are each cDNA fragment sequenced (this tells us how each read consists, for example, in 10X chromium, each read has at least two parts, read1, the technical read, and read2, the biological read), (3) how does the gel bead look like.

Best,
Dongze

[cathalgking]

BD Rhapsody v1 (27 bp barcode, 8 bp UMI)

I believe we are working with the "V1 Library" as shown in the below link. The BD library structure is analagous to the 10X chromium in that R1 is the technical read and R2 is the biological read. However, in R1, the cell label is 27 nucleotides (broken up into three 9 nucleotide sequences (CLS1-3) and separated by two 12 nucleotide linker sequences) and an 8 nucleotide UMI. I can provide some demo data if needed.

https://teichlab.github.io/scg_lib_structs/methods_html/BD_Rhapsody.html

[DongzeHE]

Hello @cathalgking ,

After discussing with @rob-p, I think we are currently able to support the V1 bead trivially. You just need to specify the chemistry when running simpleaf quant using --chemistry '1{b[9]x[12]b[9]x[12]b[9]u[8]}2{r:}'. More details about the specification language can be found at https://hackmd.io/kfRWvfjQTua42PxD_v5Vzg.

Furthermore, for me to test this, could you please also send me some demo data? Thanks so much.

Best,
Dongze

[DongzeHE]

Hi @cathalgking,

Please let me know if you encounter any problems when using the chemistry specification. Thanks.

Best,
Dongze