AIO_paper_analyis

• This repo contains the scripts for "Identification of an aberrant RNA associated with the initiation of transgene silencing" by Marianne C Kramer et al.
• This includes all data analysis steps for "All-in-One" RNA-seq, Random Forest machine learning, small RNA sequencing, and RMarkdown files for each figure in the manuscript.

Content

AIO_pipeline

• commonFiles -- Files required for data analysis that are common among all experiments. Also in this directory are the barcodes used for one example experiment (ruby_round2). Barcodes for all other experiments in this manuscript can be found in Supplemental Table 1.
• jobFiles -- jobFiles submitted for each processing step referenced in the .sh files
• .sh files are shell scripts for each data processing step outlined in AIO_pipeline_readme.md This includes running job files, QC steps, and creating directory structures to fit the analysis

Figures

• .Rmd and .md files used to generate all figures in the manuscript, that were created in R. Some panels are missing because they were not created in R (such as phenotyping images).
• There are also sub folders containing the images required to embed in .md

Random-Forest Classification modeling

• Random forest binary classification modeling using sequence features to diffrentiate phenotypes

small RNA analysis

• jobFiles -- shell scripts or slurm scripts used for data analysis, references in sRNA_readsMe.md
• sRNA_readMe.sh -- shell script of commands ran for sRNA-seq data processing
• examine_known_mirna_sites.sh -- shell script of commands ran to examine sRNA coverage at known miRNA targets -- Supplemental Figure 13.