iRAP 0.4.3d3
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 release: 79) tophat2 version: 2.0.10
htseq2 version: 0.6.1p1
(FPKMs) are calculated from the raw counts by iRAP. These are averaged for each set of technical replicates, and then quantile normalized within each set of biological replicates using limma. Finally, they are averaged for all biological replicates (if any)