How do I analyze my QuantSeq FWD-UMI Sequencing Data?

Lexogen Data Analysis Solutions

QuantSeq FWD-UMI data can be analyzed using our in-house automated Lexogen data analysis system https://lexogen-customerportal.atlassian.net/servicedesk/customer/portal/12/group/25/create/64 or our new web-based interactive platform, Kangooroo. QuantSeq kits are provided with voucher codes 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 the data analysis solutions 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:

BASH

umi_tools extract --extract-method=regex --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"

After alignment, reads can be deduplicated with the following command:

BASH

umi_tools dedup -I example.bam --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.

If you would like to run the package in a less complex way, you can set the parameter:

CODE

 "-method=unique"

This will only collapse UMIs having identical sequences.

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