canine_tumor_wes's Introduction

This repository includes all related files (codes/figures/presentations/etc.) for the canine breed prediction project during Fall 2023 in Zhao lab.
Folder structure explained below:
- scripts/: All codes for data processing and analysis. scripts/README.md includes detailed documentation for each script.
- results/: Figures and summarized result files. Detailed README files are included in each subfolder.
- metadata/: Meta tables from SRA run selector and merged meta tables to run the pipeline. README file included.
- doc/: Slides for lab meetings.

Results backup

Germline variants (in VCF), DepthOfCoverage (in BED), and QC results are backed up on cluster at /project/szlab/Jingxuan_Chen.
- /project/szlab/Jingxuan_Chen/pancaner_germline: Results for newlt published WES datasets as included in meta table metadata/data_collection_new.csv.
- /project/szlab/Jingxuan_Chen/pancaner_germline_PRJNA525883: Results for re-run of PRJNA525883, which has already been included in the original publication, but indiviual results were removed by GACRC.
Result files for breed prediction are backed up on cluster at /project/szlab/Jingxuan_Chen/breed_prediction.
Result files for phylogenetic analysis are backed up on cluster at /project/szlab/Jingxuan_Chen/phylogenetics.
Result files for WGS related results (breed specific variant identification, merge with WES results, etc.) are backed up on cluster at /project/szlab/Jingxuan_Chen/wgs_breed_prediction.
This repository is backed up on cluster at /project/szlab/Jingxuan_Chen/breed_prediction_code.

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