Processed data for the sRNA landscape chapter

Processed data to be used in analyses related to the sRNA landscape. 

1) small RNA processed data from stem trichomes: 2020-12-17_11-23_results_stem_trichomes.tar.gz

• Original small RNA-seq fastq files: available at https://doi.org/10.5281/zenodo.4105911
• Software: small-rna-seq-pipeline v0.4.4 available at https://zenodo.org/record/4333786

2) small RNA processed data from bald stem, leaf primordium and leaf:

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3) mRNA-seq processed data (raw and scaled counts) from different tissues (stem trichomes, bald stem, leaf, leaf primordium):  20201117_snakemake_messenger_rnaseq_trichomes_and_other_tissues.tar.gz

This file was obtained from the following original mRNA-seq fastq files:

• Stem trichomes of Moneymaker: dataset available here
• Stem trichomes of LA0716: dataset available here
• Stem trichomes of PI127826: dataset available here
• Bald stems, leaf primordia and leaves of Moneymaker, LA0716 and PI127826: datasets are available here. Samples S28 to S48 were used. 

The pipeline used was Snakemake RNA-seq release 0.3.4

The file contains:

• raw_counts.parsed.tsv: contains the raw counts that can be used for differential expression analysis (e.g. with DESeq2).
• scaled_counts.tsv: contains counts that are scaled between samples. This can be used for heatmap creation or PCA analysis for instance. NOT for differential analysis. 
• samples.tsv.: a file listing the fastq files analysed. 
• config.yaml: a file that contains the parameters used when running the pipeline.