RNA2M

Scripts used in Chialva et al. (2020) to analyze tomato meta-transcriptome using host RNA-seq data. If you re-use any or part of this code, please reference and cite our paper. Raw sequence data to run the script are available at NCBI-SRA under accession PRJNA422090. Intermediate results are here provided (raw counts tables) to run downstream analysis.

Scripts used to trim, filter and taxonomically annotate raw RNA-seq adapter-free reads (50bp, SE)

1.meta-transcriptome_reads_filtering_annotation.R

2.reads_counting_statistics_normalization.R

Create_taxoner_NCBI_index.sh

Scripts used for meta-transcriptome diversity analysis

3.bacteria_diversity.R

4.fungi_diversity.R

Scripts to functionally annotate reads

5.eggNOG_functional_annotation.R

Variance Partitioning Analyses

6.host_variance_partitioning.R

AM colonization analysis

7.AM_fungi.R

plots and graphics

8.plots.R

plotting_styles.R

Intermediate result files

results.tar.gz

The archive contains raw meta-transcriptome counts (taxonomy and COGs), sample meta-data mapping file, AM colonization data and plant host transcriptome normalized counts