CRISPECTOR 2.0

https://github.com/yakhinigroup/crispector2
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A genome editing analysis tool that detects, evaluates, and quantifies allele-specific on- and...
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### Verify CRISPECTOR2.0 Installation

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

Check if CRISPECTOR2.0 has been installed correctly by running its help command. This confirms the installation was successful.

```bash
crispector --help
```

--------------------------------

### Example: Run CRISPECTOR with CD33-846 Data

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

This example demonstrates running CRISPECTOR with allele analysis using specific FASTQ files and a configuration file for the CD33-846 experiment.

```bash
CRISPECTOR --allele -t_r1 CD33-846-tx-500K.r1.fastq.gz -t_r2 CD33-846-tx-500K.r2.fastq.gz -m_r1 CD33-846-mock-500K.r1.fastq.gz -m_r2 CD33-846-mock-500K.r2.fastq.gz -c CD33-846_config.csv
```

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### Install CRISPECTOR2.0 with PIP

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

Install CRISPECTOR2.0 using the PIP package manager. This method is suitable for Linux and macOS systems.

```bash
python3 -m pip install crispector2
```

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### CRISPECTOR Configuration File Example

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

Example of a CRISPECTOR configuration file snippet showing how to define parameters for indel types, specifically deletions. This includes setting minimum and maximum indel lengths and defining the prior probability for each base pair around the expected cut-site.

```yaml
Deletions:
    del_len_1:
        min: 1  # min indel length
        max: 1  # max indel length
        pos_prior: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.001, 0.1, 0.5,
                    0.5, 0.1, 0.001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001, 0.0001]
```

--------------------------------

### Install CRISPECTOR2.0 with Bioconda

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

Install CRISPECTOR2.0 into the current conda environment. This command assumes the Bioconda channels have already been added.

```bash
conda install crispector2
```

--------------------------------

### Add Bioconda Channels

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

Configure conda to use the necessary channels for installing CRISPECTOR2.0. Ensure you have Anaconda Python 3.8 installed.

```bash
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```

--------------------------------

### Create and Activate Conda Environment

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

Create a new conda environment named 'crispector_env' with Python 3.8, activate it, and then install CRISPECTOR2.0. This is useful if you don't have an existing environment.

```bash
conda create -n crispector_env python=3.8
conda activate crispector_env
conda install crispector2
```

--------------------------------

### Crispector Usage and Options

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

This snippet displays the general usage and all available options for the Crispector command-line tool. It is relevant for both multiplex and singleplex input modes.

```bash
Usage: crispector [OPTIONS]

  Accurate estimation of off-target editing activity from comparative NGS data

Options:
  -t_r1, --tx_in1 PATH            Tx read 1 input path or Tx merged FASTQ file
  -t_r2, --tx_in2 PATH            Tx read 2 input path, if FASTQ files aren't
                                  merged [OPTIONAL]
  -m_r1, --mock_in1 PATH          Mock read 1 input path or mock merged FASTQ
                                  file
  -m_r2, --mock_in2 PATH          Mock read read 2 input path, if FASTQ files
                                  aren't merged [OPTIONAL]
  -c, --experiment_config PATH    A CSV (Comma Separated Values‏) file with
                                  the experiment data. Table has 11 columns:
                                  SiteName, AmpliconReference, gRNA, OnTarget,
                                  ForwardPrimer, ReversePrimer,TxInput1Path
                                  TxInput2Path, MockInput1Path,
                                  MockInput2Path, DonorReference. The first 4
                                  columns are required, the rest are optional.
                                  Header should be specified by the above
                                  order. Please check the README on GitHub
                                  further details and examples.  [required]
  -o, --report_output PATH        Path to output folder
  --cut_site_position INTEGER     Expected cut-site position with respect to
                                  the 3' end of the provided sgRNA sequence.
                                  Note, the sgRNA sequence must be entered
                                  without the PAM.  [default: -3]
  --crispector_config PATH        Path to crispector configuration in YAML
                                  format.See "Advanced usage" section in
                                  README on GitHub for further.
  --fastp_options_string TEXT     Try "fastp --help" for more details
  --min_num_of_reads INTEGER      Minimum number of reads (per locus site) to
                                  evaluate edit events  [default: 500]
  --min_read_length_without_primers INTEGER
                                  Filter out any read shorter than
                                  min_read_length_without_primers + length of
                                  forward and reverse primers. This threshold
                                  filters primer-dimmer effect reads.
                                  [default: 10]
  --max_edit_distance_on_primers INTEGER
                                  Maximum edit distance to consider a read
                                  prefix (or suffix) as a match for a primer.
                                  [default: 8]
  --amplicon_min_score FLOAT RANGE
                                  Minimum normalized alignment score to
                                  consider a read alignment as valid.
                                  Normalized alignment score is defined as the
                                  Needleman-Wunch alignment score divided by
                                  the maximum possible score. Below this
                                  alignment threshold, reads are discarded.
                                  [default: 30; 0<=x<=100]
  --translocation_amplicon_min_score FLOAT RANGE
                                  Minimum alignment score to consider a read
                                  with primer inconsistency as a possible
                                  translocation. Should be higher than
                                  --amplicon_min_score, because translocations
                                  reads are noisier.Score is normalized
                                  between 0 (not even one bp match) to 100
                                  (read is identical to the reference)
                                  [default: 80; 0<=x<=100]
  --min_editing_activity FLOAT RANGE
                                  Minimum editing activity (%). Sites with
                                  editing activity lower than the minimum, 
                                  will be discarded from the translocation
                                  detection.  [default: 0.1; x<=None]
  --translocation_p_value FLOAT RANGE
                                  Translocations statistical significance
                                  level. This threshold is applied on the
                                  corrected p_value,FDR (false discovery
                                  rate).  [default: 0.05; x<=None]
  --disable_translocations        Disable translocations detection  [default:
                                  False]
  --override_noise_estimation     Override noise estimation with default q
                                  parameter from crispector_config file. It's

```

--------------------------------

### Run CRISPECTOR with Allele Analysis

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

This command runs CRISPECTOR with allele analysis enabled, specifying treatment and mock FASTQ files, and an experiment configuration file.

```bash
crispector --allele -t_r1 tx_R1.fq.gz -t_r2 tx_R2.fq.gz -m_r1 mock_R1.fq.gz -m_r2 mock_R2.fq.gz -c exp_config.csv
```

--------------------------------

### Run CRISPECTOR2 with Singleplex-PCR Input

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

This command initiates CRISPECTOR2 analysis using an experiment configuration file for singleplex-PCR input. Ensure the configuration file specifies the correct paths to FASTQ files.

```bash
CRISPECTOR2 --allele -c exp_config.csv
```

```bash
crispector --allele -c EMX1_config.csv
```

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### Run CRISPECTOR without Allele Analysis

Source: https://github.com/yakhinigroup/crispector2/blob/main/README.md

This command runs CRISPECTOR without allele analysis, using the same input FASTQ and configuration files.

```bash
crispector -t_r1 tx_R1.fq.gz -t_r2 tx_R2.fq.gz -m_r1 mock_R1.fq.gz -m_r2 mock_R2.fq.gz -c exp_config.csv
```
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