bowtie_to_peak
end_to_end.bowtie_to_peak(align_file, thresh=12, peak_file=None)
Convert aligned file to peaks for 5r, 5f, 3r, and 3f.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
align_file |
(required) str path to the bowtie file. | required | |
thresh |
should be used for thresholding z score values. | 12 |
|
peak_file |
(optional, default = None), str path to a peaks file. If provided peaks will be used to remove shadows from the peaks. | None |
Returns
| Type | Description |
|---|---|
| str path to the location of the peaks file. |