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WGLab / AmpBinner

A barcode demultiplexer for Oxford Nanopore long-read amplicon sequencing data
MIT License
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Improve cell barcode assignment rate #7

Open MikaQiao opened 2 years ago

MikaQiao commented 2 years ago

Hi,

I am using AmpBinner to demultiplex Nanopore sequencing data generated from the 10X V3 library. The cell barcode assignment rate is approximately 20%. Do you know how to improve it?

Thanks!

fangli80 commented 2 years ago

Hello Mika, Thank you for your question. Many 10X Genomics barcodes are very similar to each other. Given the current sequencing error rate of nanopore reads, I think it's very difficult to improve the barcode assignment rate without sacrificing accuracy. If you know other tools that have a higher barcode assignment rate, please let me know.

Thanks! Li

MikaQiao commented 2 years ago

Hi Li,

Thank you for your kind reply!

As you mentioned, due to the current sequencing error rate of nanopore reads, I combined two tools, i.e., AmpBinner with sicelore for more accurate identification of cell barcode.

The barcode assignment rate of sicelore is approximately 60%~80%.

Maybe this can help.

Best, Mika