Transcription profiling by RNA-seq during NuRD complex induction in mouse embryonic stem cells

RNA-Seq mRNA differential
Organism: Mus musculus

Analysis Methods

Pipeline version
iRAP 1.0.1
Analyzed Libraries
Filtering Step 1
Discard reads below minimum quality threshold
Filtering Step 2
Check of bacterial contamination; discard offending reads
Filtering Step 3
Discard reads with common uncalled characters (e.g. N)
Filtering Step 4
Remove reads from pair-end libraries that were orphaned by filtering steps 1-3
Read Mapping
Against genome reference (Ensembl release: 97) HISAT2 version: 2.1.0
Quantification
FeatureCounts version: 1.6.2
Differential Expression
DESeq2 version: 1.10.1
Gene Set Overlap
Fisher (non-directional), FDR < 0.1 using piano version 1.14.5

Resources