Organism(s): Oryza sativa Japonica Group
Reference(s): 22443345
iRAP 0.4.3d1
Single-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: 23) tophat2 version: 2.0.10
cufflinks2 version: 2.1.1 (no novel transcript discovery)
Obtained from the genes.fpkm_tracking files, then averaged for all biological replicates (if any)