Genome + transcriptome analysis code and corresponding files

Le résumé fourni par la source

Folders:genome_statsgenomestats_compare.R - plotting script for Fig. 4A, associated files: busco.csv, genomestats.csv, orthogroup_comparison.csvgenome_kegg_functionsparsekeggbrite.R - assign functional annotations to KEGG assignments for functional enrichment, associated files: keggmatches.csv for each of 5 genomes for comparison, output file: keggbrite_5genomes.csvRNAseq_experimentprocessing_rnaseq_reads.R - code for processing fastq rnaseq data from temperature experiment (48C v 61C), performing deseq2 analysis, and calculating transcripts-per-million (TPM) normalized counts.code for running RNAseq analysis, in order: ultils.R, 0_preprocess.R, 1_pca.R, 2_levelC_bias_grouped_final.Rbc2001_bin7_mapped.txt : per-feature tabulated raw counts mapped to the Incendi pacbio bin across each temperature replicatesample_metadata.csv: metadata associated with sample IDs in the columns of bc2001_bin7_mapped.txt . Used for deseq2 fold-change analysis between 48C and 61Cpulling_abundant_transcripts.R code for selecting most abundant/most upregulated transcriptsorthofinderoutput files from Orthofinder including Orthogroups.GeneCount.csv and Statistics_PerSpecies.csv

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.