This directory contains input data used for the analysis and configuration for some of the analyses:
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barcode_runs.csv: Illumina sequencing runs for barcode counting. The sample column should be the hyphen separated concatenation of experiment, antibody, concentration, and selection. The combination of the library and sample columns should be unique. The frac_escape column gives the overall fraction of the library that escaped antibody. The R1 FASTQ files should be semicolon (
;) separated list of glob patterns. -
wildtype_sequence.fasta: wildtype sequence of mutagenized gene.
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./pdbs/: files downloaded from the Protein Data Bank for structural analyses.
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escape_profiles_config.yaml: Information on how to plot the escape profiles; manually edit this to alter their plotting.
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output_pdbs_config.yaml: Information on how to output structural mappings of escape.
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structural_annotation_config.yaml: Information on how to output structural annotations of contact residues in various RBD:ligand complexes.
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site_color_schemes.csv: Schemes for how to color sites (can be used in escape profiles).
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spikeprot0315.tar.tar.xz: A compressed FASTA file with all spike sequences in GISAID. Downloaded on March-15-2021 as follows: logged into GISAID, went to the EpiCoV page, clicked on Downloads, clicked on spikeprot0315, which yielded the file
spikeprot0315.tar.tar.xzwhich was then copied here. -
./RBD_sites.csv: Useful numeric and functional annotations of RBD sites for referencing in various analyses.
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./RBDs_aligned.fasta: alignment of sarbecovirus RBDs.