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umi_tools extract –extract--extract-method=regex –bc--bc-pattern "(?P<umi_1>.{6})(?P<discard_1>.{4}).*" -L "/path/to/my_outputlog.txt" -I "/path/to/my_input.fastq.gz" -S "/path/to/my_output.fastq.gz" |
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umi_tools dedup -I example.bam –output--output-stats=deduplicated -S deduplicated.bam |
The deduplication method of UMI-Tools has been published here.
NOTE: The current implementation of this method can take some time and can consume significant memory. If you experience issues with run time or memory usage, please refer to these FAQs.
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