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
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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
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!
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?
Yes, it would be very helpful to see an example of the STARsolo code for MGI's technology.
Thanks
See this thread for some additional information: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
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It might be proprietary/non open source. Contact them directly.
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.