2_merge_peaks

# General workflow after CellRanger for merging

After from extract.snakefile, please see jupyter notebook for downstream processing and R work

Run this workflow after "outs" generated from CellRanger to merge all the data into 1 Seurat Object.

Note

1. If following since start, accessions.txt should be a list of ALL unique "id"s (in metadata.csv file earlier on) across experiments to be extracted. **needs to be generated by user
2. config.yaml "wd" should be your working directory.
3. The names of the output files between CellRangerARC and ATAC is different; use the right snakefile.
4. Ensure path in config.yaml ends with "/"

For successful extraction, directory structure must be as follows

.
├── extract.snakefile
├── config.yaml
├── mergePeaks_ARC.R
├── accessions.txt
├── id1
│   ├── outs
│   ├── ...
│   └── ...
└── id2
    ├── outs
    ├── ...
    └── ...

The following new folders will be created within the same directory

...
├── bed
├── filtered_matrix
├── metrics
└── frags