Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer)
The Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) template workflow supports reads captured using the ODT-RT primer protocol, where a tag of TTTV is used to capture a fragment. The short length of the polyT tag enables capture of exons as well as the polyA tail. This can be an advantage for low input samples or exosomes where exon usage can be of interest. Note that a 3' bias is not necessarily expected in the data, and only around 50% of reads may map to exons (though this depends on the sample).
The workflow provides two main outputs. The gene expression tracks, which can be used for conducting differential expression analysis, and the Genome Browser View of the mappings, useful for investigating exon usage. Note, however, that although the protocol can be used for differential expression analysis (preferably between samples with similar levels of input RNA), it does not allow for analysis of RNA abundance. This is because the measured expression is higher for genes with more polyT regions.
The Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow can be found here:
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
) | Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) (
)
Or run directly from the Analyze QIAseq Samples guide:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | Analyze QIAseq Samples (
)
where it is available in the dropdown menu of the FastSelect RNA tab by setting analysis to ODT-RT primer.
In the first wizard step either select the reads or choose Select files for import to import FASTQ files on-the-fly. Note that the FASTQ files need to be imported upfront for Analyze QIAseq Samples to work.
The workflow is designed to analyze all samples within an experiment without the need of batch functionality. It iterates through the samples and processes them separately, and collects and distributes all outputs at the end.
Choose the QIAseq UPXome and FastSelect RNA hg38 reference data when running the workflow standalone.
Keep the "Use organization of input samples" except when you want to add metadata information to the samples. Check that the batch overview looks as expected, especially when using on-the-fly import.
Save the results to a specified location.
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