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Differential Expression in total RNA and Polysomes:

RNAseq:
DEGS: gene level
in: file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/RNAseq
files taken from:
/data/images/proton/DKlab/mr/rnaseq/per-gene/

edgeRgenes_featurecount-0h.csv
edgeRgenes_featurecount-2h.csv
edgeRgenes_featurecount-6h.csv
edgeRgenes_featurecount-IFN.csv
edgeRgenes_featurecount-IL4.csv 
edgeRgenes_featurecountExpr-0h.csv
edgeRgenes_featurecountExpr-2h.csv
edgeRgenes_featurecountExpr-6h.csv
edgeRgenes_featurecountExpr-IFN.csv
edgeRgenes_featurecountExpr-IL4.csv

DETS: transcript level: 
in:file:///home/giagkas/Documents/RNAseq_Transcription/DET
from:  /data/images/proton/DKlab/mr/rnaseq/stringtie
edgeRtranscripts3-0h.csv
edgeRtranscripts3-2h.csv
edgeRtranscripts3-6h.csv
edgeRtranscripts3-IFN.csv
edgeRtranscripts3-IL4.csv
edgeRtranscripts3Expr-0h.csv
edgeRtranscripts3Expr-2h.csv
edgeRtranscripts3Expr-6h.csv
edgeRtranscripts3Expr-IFN.csv
edgeRtranscripts3Expr-IL4.csv 


Polysome seq:
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/Polysomes
DEGS: gene level
in: /data/images/proton/DKlab/mr/Polysomes/reads/stringtie/per-gene/
edgeRgenes_featurecount-0h.csv
edgeRgenes_featurecount-2h.csv
edgeRgenes_featurecount-6h.csv
edgeRgenes_featurecount-IFN.csv
edgeRgenes_featurecount-IL4.csv
edgeRgenes_featurecountExpr-0h.csv
edgeRgenes_featurecountExpr-2h.csv
edgeRgenes_featurecountExpr-6h.csv
edgeRgenes_featurecountExpr-IFN.csv
edgeRgenes_featurecountExpr-IL4.csv

DETS: transcript level: 
in:file:///home/giagkas/Documents/RNAseq_Translation/DET
from: /data/images/proton/DKlab/mr/Polysomes/reads/stringtie
edgeRtranscripts3-0h.csv
edgeRtranscripts3-2h.csv
edgeRtranscripts3-6h.csv
edgeRtranscripts3-IFN.csv
edgeRtranscripts3-IL4.csv
edgeRtranscripts3Expr-0h.csv
edgeRtranscripts3Expr-2h.csv
edgeRtranscripts3Expr-6h.csv
edgeRtranscripts3Expr-IFN.csv
edgeRtranscripts3Expr-IL4.csv

--
Plots: Expression values (RPKM) comparing KO vs WT, in abundance and translation. For Protein coding genes in total, clipped and unbound genes. For protein coding genes (biotype protein_coding, non-sense mediated decay, processed_transcript, retained intron). Threshold for RPKM values >1 for RNAseq and Polysomes seq.
*(No normalization of polysomes to total RNA seq).  
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/KO_vs_WT_rpkm.R
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/KO_vs_WT_rpkm_UnBound.R
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M0.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M0_clip.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M0_Unbound.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_2hs.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_2hs_clip.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_6hs.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_6hs_clip.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M1-IFN.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M1-IFN_CLIP.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M1-IFN_UnBound.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M2.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M2_clip.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/RPKM_poly_and_abud_PC_Keep_only_RNAseq_M2_UnBound.png

--
Attemp to normalize polysome seq to RNA seq based on zscore and RPKM values (Not used) in:
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/norm_zscore_IL4_v2.R



--
Plots: Abundance versus Translation in KO and WT using zscore for rpkm values. Use Standardised Major Axis Estimation to estimate slope difference between KO and WT. Significance (<0.05) indicates that the two lines (abundance versus translation) have similar slope.
For protein coding genes (biotype protein_coding, non-sense mediated decay, processed_transcript, retained intron). Threshold for RPKM values >1 for RNAseq and Polysomes seq.
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/smatr.R
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/M0_PC_ab_vs_transl.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/M0_PC_ab_vs_transl_v2.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/M1_PC_ab_vs_transl.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/M1_PC_ab_vs_transl_v2.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/M2_PC_ab_vs_transl.png
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/plots/M2_PC_ab_vs_transl_v2.png

--
VolcanoPlots: For abundance (RNAseq) in each condition (0hs,2hs,6hs,IFN,IL4) and threshold for RPKM>1 in wild type. For translation (polysomes seq) in each condition (0hs,2hs,6hs,IFN,IL4) and threshold for wild-typeRPKM in polysomeseq and wildtypeRPKM>1 in totalRNAseq.
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/volcanoPlots
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/volcanoPlots/volcano.R

--
DETs in DEGs:
For Abundance, differentially expressed genes with threshold  wtRPKM>1, pval<0.05, and FC>1.5 at gene level. In transcript level no RPKM,pval or FC>1.5 is applied. (RPKM values in transcript level are calculated based on  transcript length extracted from gtf file Mus_musculus.NCBIM37.64-toMM9.gtf - see merge.R. RPKM values in gene level are calculated based on average transcript length)
For Translation, differentially expressed genes with threshold  wtRPKM>1, pval<0.05, and FC>1.5 at gene level. In transcript level no RPKM,pval or FC>1.5 is applied. (RPKM values in transcript level are calculated based on  transcript length extracted from gtf file Mus_musculus.NCBIM37.64-toMM9.gtf - see merge.R. RPKM values in gene level are calculated based on average transcript length)
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/DETsinDEGs
file:///home/giagkas/Documents/norm_Polys_to_RNAseq_DEGs/DETsinDEGs/merge.R