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Lexogen Data Analysis

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Solution

Automated data analysis for QuantSeq FWD-UMI libraries is available on the BlueBee® Genomics Platform.
To analyze data from QuantSeq FWD libraries that contain UMIs, simply use the activation code included with your QuantSeq FWD library prep kit and select the respective "FWD-UMI" pipeline when setting up your data analysis run.

Be sure to only select the "FWD-UMI" pipelines for UMI-containing libraries, otherwise duplicate reads will not be collapsed.

For further details see Can I analyze my QuantSeq data using the Data Analysis Pipelines on the BlueBee® Genomics Platform? data can be analyzed using our new web-based interactive platform, Kangooroo. QuantSeq kits are provided with a voucher code which can be used for the data analysis. If additional codes are needed, please contact sales@lexogen.com.

For further information about how to process your data, please visit our Webpage https://www.lexogen.com/lexogen-data-analysis-solutions/ and check out these online FAQs.

UMI-Tools

As an alternative to BlueBeethe data analysis solution offered by Lexogen, 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:

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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For further information contact us at support@lexogen.com.