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salzman-lab / SICILIAN

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Input parameters for SICILIAN #11

Closed tjhwangxiong closed 2 years ago

tjhwangxiong commented 2 years ago

bc_pattern: this parameter is needed only for 10x data and determines the barcode/UMI pattern in R1. For V3 chemistry in which UMI has 12 bps, bc_pattern should be set to "C"*16 + "N"*12 and for 10x data based on V2 chemistry it should be set to "C"*16 + "N"*12. bc_pattern is needed for UMI_tools steps before STAR alignment on input 10x data.

The bc_pattern is the same for V2 and V3 in https://github.com/salzmanlab/SICILIAN#annotator-and-index-files-needed-for-running-sicilian section: Input parameters for SICILIAN

Is it should be: bc_pattern: this parameter is needed only for 10x data and determines the barcode/UMI pattern in R1. For V3 chemistry in which UMI has 12 bps, bc_pattern should be set to "C"*16 + "N"*12 and for 10x data based on V2 chemistry it should be set to "C"*16 + "N"*10. bc_pattern is needed for UMI_tools steps before STAR alignment on input 10x data. ?

As the UMI of V2 was 10 bp.

roozbehdn commented 2 years ago

Yes, you are right, the UMI is 10bp in V2. Thanks for finding this, we corrected the readme file.