B_viburni

Characterising the B chromosome of Pseudococcus viburni.

Regenerating paper figures and tables

Preparing directory for all figures

mkdir -p manuscript/figures_revision

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For panels of

• Figure 3: Assignment of B chromosomes

Rscript R_scripts/B_scaffod_assignment_plots.R

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For

• Figure 6: B+ vs B- gene expression analysis
• Figure S4: Distribution of library sizes and normalised log-CPMs and multi-dimensional scaling plots for the full differential expression model (sex and B presence/absence as factors)

Rscript R_scripts/B_differential_expression_plots.R

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For

• Table of annotated genes located on B scaffolds -
• Figure S3: Overall expression of B+ and B- lines

Rscript R_scripts/Exploring_AB_genes.R

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LINK Figure 1

• Figure 1: A scheme of B chromosome tranmission
• Figure 2: Staining of B chromosomes

Files

To be revised:

• output/rbbh_AB_transcripts.csv

Revised files:

• B assignment:

  • output/B_scaffold_assignment_comeplete_window_coverage_table.tsv: complete table with coverage information per 10k window
  • output/scaffolds.final.assignment.tsv: agregated table of all three sources of evidence into one table
  • output/scaffolds.final.assignment.table.csv: simplified table with assignments (scf; len; asn) - Supplementary file 1

• Gene origin & function:

  • output/B_genes.diamond_taxa_overview.tsv - diamond hits of B-genes against ncbi nr
  • output/genes.in.Bs.anno.csv - functional annotation of B-linked genes

Preprint surviving files:

• output/pviburni.gene.GO: GO terms for all genes
• output/freeze.v0.genes.anno.complete.csv: agregated functional annotation for each gene
• annotation/p.viburni.freeze.v0.braker.transcripts.to.genes.txt: gene <-> transcript table
• R_scripts/RSEM_digi.counts.matrix: expression matrix

Preprint legacy files (DO NOT USE!):

• output/scaffolds.preprint.assignment.csv: previous assignments