paper_arabidopsis_development

Sources code used in the analysis of Arabidopsis development

The shell and R scripts can be used to reproduce the processing of the RNAseq and proteomics data.

1. run_01.fastqc.raw.sh (quality control of raw data)
2. run_02.trimmomatic.sh (trimming of sequencing adapters and low quality reads)
3. run_03.fastqc.trimmed.sh (quality control of trimmed data)
4. run_04.kallisto.sh (mapping of trimmed reads to Araport11_genes.201606.cdna.fasta.gz, can be downloaded from here and indexed with kallisto index [arguments] FASTA-files)
5. run_05.txi2gene_kallisto.R (R script to collapse transcripts to gene level)
6. run_06.preprocessing_rna.DV.R (R script to normalize and filter transcript data for development datasets)
7. run_07.preprocessing_protein_DVFL.R (R script to normalize and filter proteinGroups.txt and phospho (STY)site.txt MaxQuant output data files for flower dataset)
8. run_08.preprocessing_protein_DVEB.R (R script to normalize and filter proteinGroups.txt and phospho (STY)site.txt MaxQuant output data files for seed & silique dataset)
9. run_09.preprocessing_protein_DVLF.R (R script to normalize and filter proteinGroups.txt and phospho (STY)site.txt MaxQuant output data files for leaf dataset)