Transcription profiling by high throughput sequencing of bundle sheath and leaf mesophyl from successive developmental stages of maize Mo17 inbred line
RNA-Seq mRNA baseline
Organism:
Zea mays
Publication
- Tausta SL, Li P, Si Y, Gandotra N, Liu P et al. (2014) Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes.
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: 51) HISAT2 version: 2.1.0 |
Gene Quantification | FeatureCounts version: 1.6.2 |
Transcript Quantification | kallisto version: 0.42.4 |
Normalized Counts per Gene |
Resources
