Processing Root/Shoot Pi treatment libraries

Analysis of Eutrema root and shoot RNA-seq libraries under Pi deficiency treatments, these libraries are from Yukon cabinet grown plants of single-seed descent from a Yukon field plant. Fertilization occurs weekly for 4 weeks with the respective Pi treatments, then the roots and shoots were harvested at week 4 for RNA-seq analysis.

Raw read location

cd PiLibs

Trimmed reads

cd trimOut

STAR outputs

cd STAR

QoRTs read counts

cd QoRTs

Scipts

cd scripts

Workflow

• Trim and pair reads together (trim.sh) as well as mapping them with STAR (mapping.sh), the read counting with QoRTs (QoRTs.sh)

• Meta analysis done on the properties of reads, i.e. % trimmed, % uniquely mapped (meta.sh, metaAnalysis.R)

• Retain reasonably uniquely mapped reads, i.e. mapQ ≥ 10

• Differential gene expression analysis and comparison with the Pi/S libraries (DEGs.R)