AuxinRootAtlas

Code repository for McReynolds et al., 2021

File Description:

QuantSeq_dataprocess.slurm
Script for SLURM manager that was used to perform the QuantSeq data processing:

• Trim raw reads using BBDUK
• Reads quality check using fastQC before and after trimming
• Sequence alignment to B73v4 annotation using STARaligner
• Index the alignment files using Samtools
• Extract transcript counts using HTSeq-count

Transcriptomic_analysis_PoissonSeq.Rmd
R markdown script for root tissue and auxin treatment transcript differential expression analysis:

• Uses TMM normalization
• Uses PoissonSeq for differential expression
• Outputs html file containing diagnostic plots of the data

30min_IAAvMock_upset_plot.R 120min_IAAvMock_upset_plot.R Tissue_upset_plot.R UP_IAAvMock_upset_plot_freq.R DOWN_IAAvMock_upset_plot_freq.R

R script for generating UpSet plots for characterizing overlapping and distinct sets of differentially expressed genes across samples

• Uses the UpSetR package