https://github.com/brocbyte/bioinformatics
https://github.com/brocbyte/bioinformatics
Last synced: over 1 year ago
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- Host: GitHub
- URL: https://github.com/brocbyte/bioinformatics
- Owner: brocbyte
- Created: 2022-10-22T10:09:23.000Z (over 3 years ago)
- Default Branch: trunk
- Last Pushed: 2022-11-04T06:44:33.000Z (over 3 years ago)
- Last Synced: 2025-01-05T03:49:06.214Z (over 1 year ago)
- Language: C
- Size: 59.3 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.txt
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README
# Assignment 4
1. Escherichia coli: https://www.ncbi.nlm.nih.gov/sra/SRX9196450
2. bash-script: run.sh
3. samtools flagstat res: samtools-results/GCF_000005845.2_ASM584v2_genomic_SRR12717711.txt
4. python parser script: parser.py
5. all temporary files in *-results/ folders
6.
## Snakemake Setup
to install & run:
1) install python3
2) install pip3
3) pip3 install snakemake
4) write your Snakemake file according to https://snakemake.readthedocs.io/en/stable/tutorial/basics.html
5) python3 -m snakemake -c1 {your_goal}
## Snakemake Run
cd snakemake-files
./runit.sh
7. snakemake-files/Snakemake
8. Report generated with pipeline: GCF_000005845.2_ASM584v2_genomic_SRR12717711_report.txt (obsolete, now in console)
10. snakemake-files/Snakemake
11. Report generated with pipeline: GCF_000005845.2_ASM584v2_genomic_SRR12717711_report.txt (obsolete, now in console)
12. snakemake-files/.snakemake/log (pick latest one)
13. full_dag.svg, qc_report_dag.svg
14. command for generating those file can be found in ./snakemake-files/runit.sh
full_dag.svg differs slightly from one in Assignment 4, cause "if-statement" is implemented by hand:
parse_flagstat_result rule calls ./parse.py, which will log parsed result and, if it is > 90%, will
write special file *.ok. This file is a dependency for samtools_sort rule. If parsed results was < 90%,
samtools_sort won't be executed.
also QC-report generation is fully separated and can be use as a standalone goal (see ./snakemake-files/runit.sh)