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lehner-lab / DiMSum

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
MIT License
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Requirements for use of DiMSum stages 4-5 with external count tables #11

Closed ijhoskins closed 1 year ago

ijhoskins commented 1 year ago

In the Methods section of the paper I see that WT counts are used in normalization of fitness scores:

"DiMSum calculates fitness scores of each variant i in each replicate r as the natural logarithm of the ratio between output read counts Nioutput and input read counts Niinput relative to the wild-type variant wt"

Is the WT nucleotide string to be included in the variant counts file?

For example, is line 100 of the example file the counts for the WT sequence? https://github.com/lehner-lab/DiMSum/blob/master/examples/example_variantCounts.txt

Thanks in advance for your insight!

Ian

andrefaure commented 1 year ago

Hi @ijhoskins yes that's correct. The WT nucleotide sequence must be included in the variant counts file e.g. line 100 of the example file.

ijhoskins commented 1 year ago

Thanks for your input @andrefaure !