RNA-seq of the olfactory system of newborn mice

RNA-Seq mRNA baseline
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
Gene Quantification
FeatureCounts version: 1.6.2
Transcript Quantification
kallisto version: 0.42.4
Normalized Counts per Gene
(TPMs/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)

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