RNA-seq of long poly adenylated RNA and long non poly adenylated RNA from ENCODE cell lines
RNA-Seq mRNA baseline
Organism:
Homo sapiens
Publications
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T et al. (2012) Landscape of transcription in human cells.
- Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D et al. (2011) Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.
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: 95) HISAT2 version: 2.1.0 |
Gene Quantification | FeatureCounts version: 1.6.2 |
Transcript Quantification | kallisto version: 0.42.4 |
Normalized Counts per Gene |
Resources
