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ChristofferFlensburg / superFreq

Analysis pipeline for cancer sequencing data
MIT License
110 stars 33 forks source link

RNA mode #107

Closed km-2021 closed 1 year ago

km-2021 commented 1 year ago

Hi,

"'RNA' has some minor changes when running on RNA.", what specific changes are needed?

ChristofferFlensburg commented 1 year ago

RNA as in mode="RNA" just has a few small differences in the algorithm for variant calling and copy number calling, due to differences from exomes and genomes, in particular to handle a more variable read depth in RNA-Seq. No changes are needed on your end, just set mode to RNA if you're analysing RNA-Seq data.