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improve docs
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ATpoint committed Jul 23, 2023
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Expand Up @@ -97,7 +97,7 @@ The pipeline uses (in our opinion) reasonable defaults for all processing steps.

## Output

By default, all outputs will be collected in `./atac_chip_preprocess_results/` relative to the directory from which the pipeline is launched. Use `--outdir` to change this. Outputs are:
By default, all outputs will be collected in `./atac_chip_preprocess_results/` relative to the directory from which the pipeline is launched. Use `--outdir` to change this. Output folders are:

- **alignments_filtered:** Sorted bam, bam index and flagstats for the filtered alignments.
- **alignments_unfiltered:** Sorted bam, bam index and flagstats for the unfiltered alignments.
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