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Input data

This subdirectory contains input data used by the pipeline.

PacBio full-length variant sequencing to link barcodes

PacBio_amplicon.gb: Genbank file having features to parse with alignparse. Must have gene (the gene of interest) and barcode features.

PacBio_feature_parse_specs.yaml: How to parse the PacBio amplicon using alignparse.

PacBio_runs.csv: List of PacBio CCS FASTQs used to link barcodes to variants. It must have the following columns:

  • library: name of the library
  • run: name of the sequencing run, must be unique
  • fastq: FASTQ file from running CCS

Site numbering

site_numbering_map.csv: Maps sequential 1, 2, ... numbering of the gene to a "reference" numbering scheme that represents the standard naming of sites for this gene. Also assigns each site to a region (domain) of the protein. So must have columns sequential_site, reference_site, and region.

Mutation-type classification

data/mutation_design_classification.csv classifies mutations into the different categories of designed mutations. Should have columns sequential_site, amino_acid, and mutation_type.

Neutralization standard barcodes

neutralization_standard_barcodes.csv barcodes for the neutralization standards. Must have columns barcode and name, giving the barcode and name of this neutralization standard set.

Barcode runs

barcode_runs.csv must contain the following columns (you can optionally include more):

  • sample: sample name, must be unique among barcode runs. Sample name must begin with <library>-<YYMMDD> where <library> is the library and <YYMMDD> is the date. It is recommended (but not enforced) that the full format be <library>-<YYMMDD>-<description>-<replicate> where <description> is a string description with underscores but no dashes, and <replicate> is a number.
  • library: name of library, must match a library in the barcode-variant table
  • date: date of sequencing, specified in a format parseable to a date by pandas.
  • fastq_R1: path to one more FASTQ R1 sequencing files, multiple files should be semicolon-delimited

Configuration for analyzing functional effects of mutations

func_effects_config.yml has the configuration for analyzing functional effects of mutations. The format is explained within the file.

Configuration for analyzing antibody escape

antibody_escape_config.yml has the configuration for analyzing effects of mutations on escape from antibodies or sera. The format is explained within the file.

Input data for custom analyses

./custom_analyses_data This directory contains input data for custom jupyter notebooks used in the analyses of nipah RBP DMS data and supplemental data for paper. See README in that directory for more information.