iRAP 0.6.0p4
Paired-end only
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 Plants release: 26) tophat2 version: 2.0.12
htseq2 version: 0.6.1p1
deseq2 version: 1.2.10
Fisher (non-directional), FDR < 0.1 using piano version 1.2.12