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jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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Add chartype = nucleotide to dms2_bcsubamp #32

Closed adingens closed 4 years ago

adingens commented 4 years ago

It would be process some bcsubamp sequencing data according to nucleotide rather than codon (for example, when using bcsubamp sequencing to analyze apobec hypermutation). Alternatively, we could add a codon counts to nucleotide counts function.

jbloom commented 4 years ago

@adingens: How important is the parsing of linked reads? I think we could easily add the ability to report nucleotide counts, but that will not deal with the linked reads issue. If the latter is important, maybe we should make a solution that does both immediately. If the nucleotide counts are more important, we can just do that.

jbloom commented 4 years ago

@adingens: This is now implemented in version 2.6.1.

See utils.codon_to_nt_counts: https://jbloomlab.github.io/dms_tools2/dms_tools2.utils.html#dms_tools2.utils.codon_to_nt_counts