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.

1.meta-transcriptome_reads_filtering_annotation.R

2.reads_counting_statistics_normalization.R

Create_taxoner_NCBI_index.sh

3.bacteria_diversity.R

4.fungi_diversity.R

5.eggNOG_functional_annotation.R

6.host_variance_partitioning.R

7.AM_fungi.R

8.plots.R

plotting_styles.R

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