Experiment < Expression Atlas < EMBL-EBI

RNA-seq of coding RNA of 19 human tissues from fetuses with congenital defects (NIH Roadmap Epigenomics Mapping Consortium)

RNA-Seq mRNA baseline

Organism: Homo sapiens

Publication:

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M et al. (2015) Integrative analysis of 111 reference human epigenomes.

Analysis Methods

Pipeline version	iRAP 0.7.0p1
Analyzed Libraries	See experiment design
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: 95) tophat2 version: 2.0.12
Gene Quantification	htseq 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)

Resources