/gannet/Atumefaciens/20190225_cpg_oe

Determine the Observed/Expected (O/E) ratio of CpG in set of FastA files.

Process was performed in a Jupyter Notebook (GitHub):

https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190225_swoose_CpG_OE.ipynb

---
FILES

- 20190226_join_ID_CpGs.sh: Bash script to combine results from FastA CpG O/E.

- Combined.*_analysis: Output folders for each FastA file. Each directory contains the following files:

C (count of Cs in sequences)
CG (count of CGs in sequences)
*_tab (FastA to tab file created with seqkit)
*_tab2 (Just sequences from each entry within the FastA)
G (count of Gs in sequences)
ID_CpG (initial CpG O/E determination - no header)
ID_CpG_labelled (CpG O/E determination - with header)
comb (Tabbed FastA with seq lengths, CG/C/G counts)

- ID_CpG_labelled_all: Tab-delimited text file of combined CpG O/E data for all files.

---

Notebook:

https://robertslab.github.io/sams-notebook/2019/02/26/Data-Wrangling-CpG-OE-Calculations-on-C.virginica-Genes.html