- 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.
-
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 tablemetadata/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.
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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
.