A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage
RNA-Seq mRNA baseline
Organism:
Arabidopsis thaliana
Publication
- Adrian J, Chang J, Ballenger CE, Bargmann BO, Alassimone J et al. (2015) Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.
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 Genomes release: 44) HISAT2 version: 2.1.0 |
Gene Quantification | FeatureCounts version: 1.6.2 |
Transcript Quantification | kallisto version: 0.42.4 |
Normalized Counts per Gene |
Resources
