Scripts and Annotation Files for Metatranscriptomic Profiling of Salmon Gill Microbiota

OverviewThis repository contains the scripts and processed data used for the reanalysis of publicly available poly(A)-selected RNA-seq data from Atlantic salmon gill tissue, focusing on microbial signatures detectable in unmapped reads.No new sequencing data were generated as part of this study. Sequencing dataThe RNA-seq data analyzed in this study are publicly available at the European Nucleotide Archive (ENA) under the following accession: ENA project: PRJEB47441These data were generated previously and were reanalyzed here in a retrospective manner. Contents of this repository1. Analysis scriptsanalysis_microbiome.RR script implementing all analytical steps described in the manuscript, including:Import of Kraken2 output files Construction of the phyloseq objectDifferential abundance analysis using ANCOM-BC2Alpha and beta diversity analysesGeneration of figures and summary tables2. Sample metadataAkira_Tables_LG.xlsxExcel file containing sample metadata used in the analysis (sample IDs, tank, sex, survival status).The sheet “1.Sample info” is used by the R script.3. Kraken outputThe directory krk contains all Kraken2 classification outputs for the metatranscriptome samples used in this study. For each sample, Kraken2 produced two files:*.kraken2.report.tsv: Kraken2 classification summary file, providing clade-level taxonomic counts for each detected taxon.*.kraken2.species.tsv: Species-level assignment file, listing individual reads that were classified to species-level taxa. Kraken2 classification was performed using a custom reference database described in the manuscript.The Kraken2 database itself is not included here due to size and distribution constraints; however, all scripts and parameters required to reproduce the analysis are provided.All results can be regenerated using the scripts in this repository together with the ENA data accession listed above.