Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?

Question

[benjamin.pyenson]

Hi,

I am trying to use STARsolo to process some fastq files generated using MGI's technology (DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set). In order to do so, I need a copy of the whitelist of cell barcodes. Does anyone know where this whitelist might be published? I cannot find it online anywhere easily.

In case you're wondering what cell barcodes and whitelists are, please see this link from 10X genomics: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist-

Thanks,

Ben

[Ram]

It might be proprietary/non open source. Contact them directly.

[GenoMax]

Looks like the software they provide for analysis is available: https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software

You may need to download this and see if you can find the lists or process your data via the software to see if you can discern valid barcodes.

Answer 1

[Ram]

They seem to have the whitelist(s) in a JSON file for some weird reason: https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software/blob/master/config/DNBelabC4_scRNA_readStructure.json

[benjamin.pyenson]

Hi,

I spoke with a colleague who informed me that the above link to the whitelist is accurate for DNBelab C Series. MGI has not responded to confirm/clarify anything. Thank you!

[atowns21]

could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the whitelist?

[alfonsosaera]

Yes, it would be very helpful to see an example of the STARsolo code for MGI's technology.

Thanks

[GenoMax]

See this thread for some additional information: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?