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LBMC
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hic
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de26b8fa
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de26b8fa
authored
1 year ago
by
Mia Croiset
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update usage readme with saving options
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docs/README.md
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docs/hicstuff_usage.md
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docs/README.md
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#
nf-core/hic
: Documentation
#
Meta HiC pipeline
: Documentation
The
nf-core/hic documentation
is split into the following pages:
The
Meta HiC pipeline
is split into the following pages:
-
[
Usage
](
usage.md
)
-
An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
-
[
Usage hicpro workflow
](
usage.md
)
-
An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicpro workflow.
-
[
Usage hicstuff workflow
](
hicstuff_usage.md
)
-
An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicstuff workflow.
-
[
Output
](
output.md
)
-
An overview of the different results produced by the pipeline and how to interpret them.
-
/!
\T
O UPDATE/!
\
An overview of the different results produced by the pipeline and how to interpret them.
You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website:
[
https://nf-co.re
](
https://nf-co.re
)
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@@ -124,6 +124,14 @@ Default: '--very-sensitive-local'
--hicstuff_bwt2_align_opts
'[Options for bowtie2 mapping on full reads]'
```
#### `--save_bam`
If specified, save BAM files after mapping. Default: false
```
bash
--save_bam
```
### Fragment enzyme
#### `--hicstuff_min_size`
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@@ -168,6 +176,14 @@ Name of fragments plot file. Default: 'frags_hist.pdf'
--hicstuff_frags_plot_path
'[Name of fragments plot file]'
```
#### `--save_fragments`
If specified, save fragments file. Default: false
```
bash
--save_fragments
```
### Bam2pairs
#### `--hicstuff_valid_pairs`
...
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@@ -193,6 +209,15 @@ Minimum mapping quality required to keep a pair of Hi-C reads. Default:30
[
#### `--hicstuff_circular`
](
#hicstuff_circular
)
#### `--save_pairs`
If specified, save pair files. Default: false
```
bash
--save_pairs
```
### Matrix
#### `--hicstuff_matrix`
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@@ -324,3 +349,11 @@ If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If
--filter_pcr_picard
```
#### `--save_bam_intermediates`
If specified, save BAM files after PICARD pcr filtering. Default: false
```
bash
--save_bam_intermediates
```
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@@ -400,6 +400,22 @@ Note that in this case the `--min_mapq` parameter is ignored.
--keep_multi
```
#### `--save_bam_intermediates`
If specified, save BAM files after PICARD pcr filtering. Default: false
```
bash
--save_bam_intermediates
```
#### `--save_pairs`
If specified, save pair files. Default: false
```
bash
--save_pairs
```
## Genome-wide contact maps
Once the list of valid pairs is available, the standard is now to move on the
`cooler`
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--save_aligned_inermediates
```
### `--save_bam`
If specified, save BAM files after mapping. Default: false
```
bash
--save_bam
```
### `--save_interaction_bam`
If specified, write a BAM file with all classified reads (valid pairs,
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@@ -231,7 +231,7 @@
},
"save_bam_intermediates"
:
{
"type"
:
"boolean"
,
"description"
:
"Save
BAM files PICARD pcr duplicates filtering"
"description"
:
"Save BAM files PICARD pcr duplicates filtering"
},
"save_pairs"
:
{
"type"
:
"boolean"
,
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