Organism: Arabidopsis thaliana
Reference(s): 23275579 (Filter by genes in paper)    
iRAP 0.7.0p12
See experiment design
Discard reads below minimum quality threshold
Check of bacterial contamination; discard offending reads
Discard reads with common uncalled characters (e.g. N)
Remove reads from pair-end libraries that were orphaned by filtering steps 1-3
Against genome reference (Ensembl Ensemblgenomes.org/pub/DOTrelease-RELNO/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.RELNO.gtf.gz release: 26) tophat2 version: 2.0.12
htseq2 version: 0.6.1p1
DESeq2 version: 1.10.1
Fisher (non-directional), FDR < 0.1 using piano version 1.10.2