RNA-seq of 6 tissues from Mus musculus to investigate the evolution of gene expression levels in mammalian organs

RNA-Seq mRNA baseline
Organism: Mus musculus
Publication:

Analysis Methods

Pipeline version
iRAP 0.8.5p3
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: 91) tophat2 version: 2.1.1
Gene Quantification
htseq2 version: 0.6.1p1
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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