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Code used in Fishman et al 2024

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Apache-2.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 70 Commits
.ipynb_checkpoints		.ipynb_checkpoints
Edit_site_analysis.ipynb		Edit_site_analysis.ipynb
Edit_site_analysis_M13_219_224_key.xls		Edit_site_analysis_M13_219_224_key.xls
Edit_site_analysis_demo_key.xls		Edit_site_analysis_demo_key.xls
Edit_site_analysis_example_key.xls		Edit_site_analysis_example_key.xls
LICENSE		LICENSE
README.md		README.md
demultiplexing_module.py		demultiplexing_module.py
double_Edit_site_analysis.ipynb		double_Edit_site_analysis.ipynb
edit_site_analysis_functions.py		edit_site_analysis_functions.py
edit_site_analysis_script.py		edit_site_analysis_script.py
editing_analysis_demo_output.xlsx		editing_analysis_demo_output.xlsx
gp17_expt_Edit_site_analysis.ipynb		gp17_expt_Edit_site_analysis.ipynb
gp17_expt_file_key.xlsx		gp17_expt_file_key.xlsx
gp17_pre_post_analysis.ipynb		gp17_pre_post_analysis.ipynb
gp17_pre_post_key.xlsx		gp17_pre_post_key.xlsx
individual_recode_edits.ipynb		individual_recode_edits.ipynb
insertions_deletions_editing_file_key.xlsx		insertions_deletions_editing_file_key.xlsx
msCF_02_134.fastq		msCF_02_134.fastq
msCF_02_135.fastq		msCF_02_135.fastq
msSBK_34_01.fastq		msSBK_34_01.fastq
msSBK_34_02.fastq		msSBK_34_02.fastq
msSBK_34_25.fastq		msSBK_34_25.fastq
msSBK_34_26.fastq		msSBK_34_26.fastq
phage_insertions_deletions.py		phage_insertions_deletions.py
recode_Edit_site_analysis.ipynb		recode_Edit_site_analysis.ipynb
test_phage_insertions_deletions.py		test_phage_insertions_deletions.py
wrapper_phage_insertions_deletions.py		wrapper_phage_insertions_deletions.py

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System Requirements
Jupyter (jupyter.org) running Python 3
All other dependencies contained within .ipynb files (e.g. Bio.SeqIO, pandas, fuzzysearch, pickle, matplotlib) can be installed using pip
Installation Guide
Clone Project or download individual analysis files
Typical install time: 1-20 minutes
Demo
Run Edit_site_analysis.ipynb on example fastq files provide in the repo using the sample key "Edit_site_analysis_demo_key.xls" also provided in repo
Editing percentages will be generated in a pandas dataframe and exported to an xlsx file named "editing_analysis_demo_output.xlsx"
Expected run time <5 minutes
Instructions for Use
Use individual analysis .ipynb files, which require fastq or fastq.gz files and descriptions of the editing site(s) provided in accompanying sample key (see demo)

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