The scripts and data used in the work "Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host" are organized as followin: 
	
1) Performance analyses: folder "survival" (survival.tar.gz, compressed).

	Main script: development_survival_plastic.Rmd 
	HTML report style template: custom.css  

	 
2) RNASeq analyses (RNASeq.tar.gz) folders:

	i. analysis: 
		Main script: RNASeqPepper.Rmd 
		HTML report style template: custom.css  

	ii. ref:
		Reference files: GCF_001854935.1_ASM185493v1_*.* (Bemisia tabaci RefSeq files), gene_list_ncbi.tab, MEAM1_ReafSeq_GO.tab, MEAM1_interpro.tsv.
			--> GCF_001854935.1_ASM185493v1_genomic_mod.gff: modified gff without tRNAs to avoid RSEM problems with missing gene IDs.  
		RSEM/HISAT 2 index files: BeTa_RefSeq.* 
		Auxiliary scripts: intepro.sh, interpro2toGO.py (reads results from interpro in tsv and return a tabular file of genes and associated GOs)

	iii. exp: generated dunring the mapping to store BAM and count matrix files. BAM and intermediate files are not supplied for storage reasons. Only count matrices are supplied. BAM and intermediate files can be obtained running the main R script (change eval=F to eval=T at each chunck preamble). 

	iv. fastq: all required fastq files