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sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
MIT License
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Short read data requirement #162

Closed rsalz closed 1 year ago

rsalz commented 1 year ago

Can this pipeline be run without short-read data? I see kallisto output from short read data is a required input of the pipeline. I only have long-read data but would still like to use this.

gsheynkman commented 1 year ago

Yes, the pipeline is most commonly run without short-read data input. Simply do not run the steps that require SR data. Or, input "dummy" SR data and ignore the final result of TPM values.