@Jianyu Yang, Pennsylvania State University
General rules could be used for specific purpose
The following files could be expected from this general pipeline:
- output/mapped/{sample}-{rep}.merge.bam
- output/mapped/{sample}-{rep}-{unit}.flag.bam
- output/qc/multiqc/multiqc.html
- output/qc/bamPEFragmentSize/{sample}-{rep}.hist.png
- output/coverage/{sample}-{rep}.bgToBw.bw
- output/coverage/{sample}-{rep}.bamCov.bw
- output/coverage/{sample}-{rep}.bamCompare.bw
Workflows supported by this general pipeline:
| Name | Description |
|---|---|
| chip-seq-standard-pipeline | For ChIP-seq, MNase-seq analysis |
| atac-seq-standard-pipeline | For ATAC-seq analysis |
| dna-methylation-pipeline | For BS-seq, TAB-seq, methylC-seq (Bismark seems not working during some steps due to the environment issue) |
Change log:
- Feb 25, 2022: Job grouping for cluster execution (Reverted due to cpu management performance issue)
- Dec 21, 2021: Signal coverage profile around TSS integrated
- Nov 23, 2021: Snakemake report feature integrated
- Nov 20, 2021: All snakemake pipelines have been integrated with cookiecutter, to motivates easily deployment of pipeline