Dear Margarita and George,

the reprocessing of the RNAseq data has finished.
We have slightly higher sensitivity:
Hisat2 alignments:
     Matching intron chains:   80149
       Matching transcripts:   93343
              Matching loci:   36292
 Total union super-loci across all input datasets: 38729 
121784 out of 121784 consensus transcripts written in compare1.annotated.gtf (0 discarded as redundant)

Old alignments:
     Matching intron chains:   80149
       Matching transcripts:   93343
              Matching loci:   36292
 Total union super-loci across all input datasets: 37492 
106411 out of 106411 consensus transcripts written in compare1.annotated.gtf (0 discarded as redundant)

Results are at:
https://genomics-lab.fleming.gr/fleming/DKlab/mr/rnaseq/stringtie2/

Counts per gene per sample:
gene_counts_merged3.txt

edgerR diff.exp. results:
edgeRgenes_featurecount-0h.csv 
edgeRgenes_featurecount-2h.csv 
edgeRgenes_featurecount-6h.csv 
edgeRgenes_featurecount-IFN.csv
edgeRgenes_featurecount-IL4.csv