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34 changes: 19 additions & 15 deletions docs/readme/benchmark.md
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Expand Up @@ -12,44 +12,48 @@ maxatac benchmark --prediction GM12878_CTCF_chr1.bw --gold_standard GM12878_CTCF

### `--prediction`

The input bigwig file of transcription factor binding predictions. This file can also be any bigwig signal track that you want to compare against a gold standard.
The input bigWig file of transcription factor binding predictions. This file can also be any bigWig signal track that you want to compare against a gold standard.

### `--gold_standard`

The input gold standard bigwig file. This file needs to be a binary signal track that has 1 corresponding to TFBS (e.g., from ChIP-seq) and 0 in positions with no TFBS.
The input gold standard bigWig file. This file needs to be a binary signal track that has 1 corresponding to TFBS (e.g., from ChIP-seq) and 0 in positions with no TFBS.

### `--prefix`

The output filename prefix to use. Default: `maxatac_benchmark`

## Optional Arguments

### `--chromosomes`
### `--agg`

The method to use for aggregating the single base-pair predictions into larger bins. Options include `max`, `min`, and `mean`. Default: `max` score found in the window.

The chromosomes to benchmark the predictions for. Default: `chr1` is the held out test chromosome.
See the [pyBigWig documentation](https://github.com/deeptools/pyBigWig#compute-summary-information-on-a-range) for more details.

### `--bin_size`

The size of the bin to use for aggregating the single base-pair predictions. Default: `200` is the size used by the [ENCODE-DREAM in vivo TFBS Prediction Challenge](https://www.synapse.org/#!Synapse:syn6131484/wiki/402026)

### `--agg`
### `--blacklist_bw`

The method to use for aggregating the single base-pair predictions into larger bins. Options include `max`, `min`, and `mean`. Default: `max` score found in the window.
The path to the blacklist bigWig signal track of regions that should be excluded. Default: `hg38_maxatac_blacklist.bw`, which contains regions that are specific to ATAC-seq.

See the [pyBigWig documentation](https://github.com/deeptools/pyBigWig#compute-summary-information-on-a-range) for more details.
### `--chromosomes`

### `--round_predictions`
The chromosomes to benchmark the predictions for. Default: `chr1` is a held-out test chromosome.

This flag will set the precision of the predictions signal track. Provide an integer that represents the number of floats before rounding. Currently, the predictions go from `0 - .0000000001`. Default: `9` is the limit of precision from TensorFlow.
### `--genome`

### `--output_directory`
The genome build that was used for the prediction file. Default: hg38.

The output directory to write the results to. Default: `./prediction_results`
### `--loglevel`

### `--blacklist_bw`
This argument is used to set the logging level. Currently, the only working logging level is `ERROR`.

### `--output_directory`

The path to the blacklist bigwig signal track of regions that should be excluded. Default: `hg38_maxatac_blacklist.bed` which contains regions that are specific to ATAC-seq.
The output directory to write the results to. Default: `./prediction_results`

### `--loglevel`
### `--round_predictions`

This argument is used to set the logging level. Currently, the only working logging level is `ERROR`.
This flag will set the precision of the predictions signal track. Provide an integer that represents the number of floats before rounding. Currently, the predictions go from `0 - .0000000001`. Default: `9` is the limit of precision from TensorFlow.