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csf-ngs / surecellumi

extraction of Illumina SureCell UMI protocol. Compatible with umi-tools

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umi-tools compatibility

jakubovciak opened this issue · comments

commented

Hi,
nice tool, already tried on my own data. But it is not clear to me in which step do you introduce this tool to umi-tools pipeline? I'd intuitively use your tool instead of the umi-tools extract command. But does your tool corrects mismatched cell barcodes and is the CB and UMI format in read headers compatible with umi-tools count?