Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)
Default: 0
Default: 20
```bash
--cutsite_seed'[Size of fragment]'
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...
@@ -375,11 +375,11 @@ Name of distance law table plot if hicstuff_distance_plot is true. Default: dist
--hicstuff_distance_out_plot'[Name of distance law plot file]'
```
#### `--hicstuff_filter_pcr`
#### `--filter_pcr`
If true, PCR duplicates will be filtered based on genomic positions Pairs where both reads have exactly the same coordinates are considered duplicates and only one of those will be conserved. Default: false
```bash
--hicstuff_filter_pcr
--filter_pcr
```
> :warning: **Warning**: if true, `--filter_pcr_picard` **must** be false
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@@ -392,7 +392,7 @@ Name of pair file after PCR filtering. Default: 'valid_idx_pcrfree.pairs'
#### `--filter_pcr_picard`
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--hicstuff_filter_pcr`**must** be false. Default:'false'
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--filter_pcr`**must** be false. Default:'false'