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As an alternative to BlueBee, we recommend utilizing the publicly available UMI-Tools package available on GitHub here. Detailed documentation can be found in the ReadTheDocs. The following command line will extract the UMI sequence from the read while removing the adjacent 4 nt TATA spacer:
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umi_tools extract –extract-method=regex –bc-pattern "(?P<umi_1>.{6})(?P<discard_1>TATA1>.{4}).*" -L "/path/to/my_outputlog.txt" -I "/path/to/my_input.fastq.gz" -S "/path/to/my_output.fastq.gz"' |
After alignment, reads can be deduplicated with the following command:
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umi_tools dedup -I example.bam –output-stats=deduplicated -S deduplicated.bam |
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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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