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Update README #424

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122 changes: 62 additions & 60 deletions README.md
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[![Docker Cloud Automated build](https://img.shields.io/docker/cloud/automated/pinellolab/crispresso2.svg)](https://hub.docker.com/r/pinellolab/crispresso2)
[![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/pinellolab/crispresso2.svg)](https://hub.docker.com/r/pinellolab/crispresso2)
[![Docker Image Version (tag)](https://img.shields.io/docker/v/pinellolab/crispresso2/latest?logo=docker&label=Docker)
](https://hub.docker.com/r/pinellolab/crispresso2/tags)
[![CircleCI branch](https://img.shields.io/circleci/project/github/pinellolab/CRISPResso2/master.svg)](https://circleci.com/gh/pinellolab/CRISPResso2)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/crispresso2/README.html)

Expand Down Expand Up @@ -167,64 +167,15 @@ docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPResso --fastq

Guardrails automatically check the inputs and results of experiments against standardized values. The guardrail warnings that are triggered are printed in the commandline and at the top of generated reports. In order to turn off the guardrails, add the `--disable_guardrails` argument.

TotalReadsGuardrail : Checks if the number of reads is lower than expected. (Default: 10000)
OverallReadsAlignedGuardrail : Checks if the number of aligned reads is lower than expected. (Default: 90% of the total reads)
DisproportionateReadsAlignedGuardrail : Checks if the number of reads aligned to an amplicon is higher or lower than expected proportionally. (Default: 30% more or less than expected)
LowRatioOfModsInWindowToOutGuardrail : Checks if the ratio of modifications inside to outside the quantification window is lower than expected. (Default: 0.01)
HighRateOfModificationAtEndsGuardrail : Checks if there is a high rate of modifications at the ends of the read. (Default: 0.01)
HighRateOfSubstitutionsOutsideWindowGuardrail : Checks if there is a high rate of substitutions outside of the quantification windows. (Default: 0.002)
HighRateOfSubstitutionsGuardrail : Checks if the proportion of substitutions to other modifications is higher than expected. (Default: 0.3)
ShortSequenceGuardrail : Checks if the provided sequences (both Amplicons and Guides) are shorter than expected. (Amplicon Default: 50, Guide Default: 19)
LongAmpliconShortReadsGuardrail : Checks if the rovided amplicon is more than <value> times the average length of read. (Default: 1.5)

### CRISPRessoPro

CRISPResso is an open source tool for free use by academics. However, for-profit organizations are required to purchase a license to use CRISPResso. As a part of this license, organizations gain access to the CRISPRessoPro package which supplements CRISPResso
with several useful features:
- Interactive and improved plots using D3 and Plotly
- Customizable colors
- Customizable warnings based on potential issues in results (guardrails)

#### Installation

To add CRISPRessoPro to CRISPResso contact Edilytics - support@edilytics.com

#### D3 and Plotly

If CRISPRessoPro is installed, by default reports will include interactive plots. To use matplotlib for figures add the `--use_matplotlib` argument.

#### Customizable Colors and Guardrails

If CRISPRessoPro is installed, by default the colors and guardrails will remain the same as CRISPResso. To alter this, use the `--custom_config` argument and a filepath to a `.json` file with the following format:

'''
"colors": {
'Substitution': '#0000FF',
'Insertion': '#008000',
'Deletion': '#FF0000',
'A': '#7FC97F',
'T': '#BEAED4',
'C': '#FDC086',
'G': '#FFFF99',
'N': '#C8C8C8',
'-': '#1E1E1E',
},
"guardrails": {
'min_total_reads': 10000,
'aligned_cutoff': 0.9,
'alternate_alignment': 0.3,
'min_ratio_of_mods_in_to_out': 0.01,
'modifications_at_ends': 0.01,
'outside_window_max_sub_rate': 0.002,
'max_rate_of_subs': 0.3,
'guide_len': 19,
'amplicon_len': 50,
'amplicon_to_read_length': 1.5
}
'''
(These are the default values as an example).

Change the values as desired to any color or guardrail specification.
- `TotalReadsGuardrail` Checks if the number of reads is lower than expected. (Default: 10000)
- `OverallReadsAlignedGuardrail` Checks if the number of aligned reads is lower than expected. (Default: 90% of the total reads)
- `DisproportionateReadsAlignedGuardrail` Checks if the number of reads aligned to an amplicon is higher or lower than expected proportionally. (Default: 30% more or less than expected)
- `LowRatioOfModsInWindowToOutGuardrail` Checks if the ratio of modifications inside to outside the quantification window is lower than expected. (Default: 0.01)
- `HighRateOfModificationAtEndsGuardrail` Checks if there is a high rate of modifications at the ends of the read. (Default: 0.01)
- `HighRateOfSubstitutionsOutsideWindowGuardrail` Checks if there is a high rate of substitutions outside of the quantification windows. (Default: 0.002)
- `HighRateOfSubstitutionsGuardrail` Checks if the proportion of substitutions to other modifications is higher than expected. (Default: 0.3)
- `ShortSequenceGuardrail` Checks if the provided sequences (both Amplicons and Guides) are shorter than expected. (Amplicon Default: 50, Guide Default: 19)
- `LongAmpliconShortReadsGuardrail` Checks if the provided amplicon is more than `<value>` times the average length of read. (Default: 1.5)

### Example run: Non-homologous end joining (NHEJ)

Expand Down Expand Up @@ -1235,3 +1186,54 @@ The output will consist of:
3. CRISPRessoAggregate_mapping_statistics.txt: A tab-separated file showing the number of reads sequenced and mapped for each run.
4. CRISPRessoAggregate_quantification_of_editing_frequency.txt: A tab-separated with the number of reads and edits for each run folder. Data from run folders with multiple amplicons show the sum totals for all amplicons.
5. CRISPRessoAggregate_quantification_of_editing_frequency_by_amplicon.txt: A tab-separated file showing the number of reads and edits for each amplicon for each run folder. Data from run folders with multiple amplicons will appear on multiple lines, with one line per amplicon.

### CRISPRessoPro

CRISPResso is an open source tool for free use by academics. However, for-profit organizations are required to purchase a license to use CRISPResso. As a part of this license, organizations gain access to the CRISPRessoPro package which supplements CRISPResso
with several useful features:

- Interactive and improved plots using D3 and Plotly
- Customizable colors
- Customizable warnings based on potential issues in results (guardrails)

#### Installation

To add CRISPRessoPro to CRISPResso contact Edilytics - licensing@edilytics.com

#### D3 and Plotly

If CRISPRessoPro is installed, by default reports will include interactive plots. To use matplotlib for figures add the `--use_matplotlib` argument.

#### Customizable Colors and Guardrails

If CRISPRessoPro is installed, by default the colors and guardrails will remain the same as CRISPResso. To alter this, use the `--config_file` argument and a filepath to a `.json` file with the following format:

``` json
{
"colors": {
"Substitution": "#0000FF",
"Insertion": "#008000",
"Deletion": "#FF0000",
"A": "#7FC97F",
"T": "#BEAED4",
"C": "#FDC086",
"G": "#FFFF99",
"N": "#C8C8C8",
"-": "#1E1E1E"
},
"guardrails": {
"min_total_reads": 10000,
"aligned_cutoff": 0.9,
"alternate_alignment": 0.3,
"min_ratio_of_mods_in_to_out": 0.01,
"modifications_at_ends": 0.01,
"outside_window_max_sub_rate": 0.002,
"max_rate_of_subs": 0.3,
"guide_len": 19,
"amplicon_len": 50,
"amplicon_to_read_length": 1.5
}
}
```

Above are the default values as an example, change the values as desired to any color or guardrail specification.
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