Lexogen Data Analysis Solutions
Lexogen offers data analysis solutions for QuantSeq FWD-UMI libraries.
Starting from January 2023, to analyze data from QuantSeq FWD libraries that contain UMIs, use the activation code included in your QuantSeq FWD library prep kit and follow the instruction provided in this online FAQ for submitting your Data Analysis Request.
For further details see How can I analyze my QuantSeq data using Lexogen data analysis solutions?
For updates on the data analysis solutions provided by Lexogen, please check this Webpage: Lexogen Data Analysis Solutions | Lexogen
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:
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:
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:
"-method=unique"
This will only collapse UMIs having identical sequences.
For further information contact us at support@lexogen.com.