File_name 	Associated_script 	Description 
Script1_fig1.html	1	"HTML documented generated by the Script1_fig1.rmd. Document shows data processing, graphs and associated statistical methods with pointers to the main text."
Script1_fig1.rmd	na	Rnotebook  for generateing figure 1. Unparsed differential gene expression.
Script2_fig2.html	2	"HTML documented generated by the Script2_fig2.rmd. Document shows data processing, graphs and associated statistical methods with pointers to the main text."
Script2_fig2.rmd	na	Rnotebook  for generateing figure 2. Allele specific expression analysis.
Script3_fig3.html	3	"HTML documented generated by the Script3_fig3.rmd. Document shows data processing, graphs and associated statistical methods with pointers to the main text."
Script3_fig3.rmd	na	Rnotebook  for generateing figure 3. Coding SNP analysis
Script4_fig4.html	4	"HTML documented generated by the Script4_fig4.rmd. Document shows data processing, graphs and associated statistical methods with pointers to the main text."
Script4_fig4.rmd	na	Rnotebook  for generateing figure 4. TFBS analysis.
CV_complete_countmatrix.txt	"1,2"	"Not included here but can be downloaded from NCBI Gene Expression Omnibus , accession number GSE155033."
gene_symbol_conversions4.tsv	"1,2"	Flybase/Gene name/RefSeqID conversion table.
immunelist_LB_2019_cat.txt	"1,2,4"	"List of immune genes pooled from De Gregorio et al., 2001; Lemaitre and Hoffman 2007; Troha et al., 2018."
tf_Celniker2013_v2.txt	"1,2"	List of known drosophila transcription factors from Hammonds 2013.
cv7_iso1_meta.txt	1	Unparsed sample meta data.
efae_imgcatfdr05.txt	1	List of gene and group assignments for Efae responsive genes. This file is technically generated by this script but is included here in case the user does not feel like running all both treatment conditions to generate the necessary files.
immgenes_efaefdr05.txt	1	List of verified immune genes found in Efae responsive genes. This file is technically generated by this script but is included here in case the user does not feel like running all both treatment conditions to generate the necessary files.
smar_imgcatfdr05.txt	1	List of gene and group assignments for smar responsive genes. This file is technically generated by this script but is included here in case the user does not feel like running both treatment conditions to generate the necessary files.
immgenes_smarfdr05.txt	1	List of verified immune genes found in smar responsive genes. This file is technically generated by this script but is included here in case the user does not feel like running both treatment conditions to generate the necessary files.
cv_asap_meta.txt	2	Parsed sample metadata
dm6_chrXrefGenes.txt	2	Drosophila x chromosome genes
poi01_genes.txt	2	High confidence genes to use for the analysis ( see methods) 
control_signal.txt	2	File of cis and trans effects in the control sample. This file is technically generated by this script but is included here in case the user does not feel like running all 3 treatment conditions to generate the necessary files.
efae_cistrans.txt	2	File of cis and trans effects in the Efae sample. This file is technically generated by this script but is included here in case the user does not feel like running all 3 treatment conditions to generate the necessary files.
smar_cistrans.txt	2	File of cis and trans effects in the smar sample. This file is technically generated by this script but is included here in case the user does not feel like running all 3 treatment conditions to generate the necessary files.
signal_comp.txt	2	Summary of cis and trans effects in each treatment.
expressed.txt	3	VEP predictions for all expressed genes in the fat body.
detreated.txt	3	VEP predictions for deferentially expressed genes in the fat body in response to infection.
deimmune.txt	3	VEP predictions for deferentially expressed immune genes in the fat body in response to infection.
transcources.txt	3	VEP predictions for 22 potential trans source genes
exnonDEimm.txt	3	VEP predictions for immune genes detected in the fat body that were NOT differentially expressed in response to infection.
senger_2004_bs.txt	4	Binding sites Identified identified by Senger et al 2004
fimo_a4_try2p001.tsv	4	FIMO output for A4 regions(pvalue threshold of p=.001)
fimo_b6_try2p001.tsv	4	FIMO output for B6 regions(pvalue threshold of p=.001)
fimo_a4_try2p0001.tsv	4	FIMO output for A4 regions(pvalue threshold of p=.0001)
fimo_a4_try2p0001.tsv	4	FIMO output for B6 regions(pvalue threshold of p=.0001)