---
name: "Bio::Tradis::RunTradis"
section: "3pm"
platform: "linux"
package: "bio-tradis"
version: "1.4.5+dfsg2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tradis::RunTradis"
---

# Bio::Tradis::RunTradis(3pm)

Perform all steps required for a tradis analysis

## NAME

Bio::Tradis::RunTradis - Perform all steps required for a tradis analysis

## VERSION

version 1.4.5

## SYNOPSIS

Takes a fastq file with tags already attached, filters the tags matching user input, removes the tags, maps to a reference (.fa) and generates insertion site plots for use in Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis.

```
   use Bio::Tradis::RunTradis;

   my $pipeline = Bio::Tradis::RunTradis->new(
                                        fastqfile => 'abc',
                                        reference => 'abc',
                                        tag => 'abc',
                                        tagdirection => '5'|'3'
   );
   $pipeline->run_tradis();
```

## PARAMETERS

### Required

- •

  `"fastqfile"` - file containing a list of fastqs (gzipped or raw) to run the \
   			complete analysis on. This includes all (including \
   			intermediary format conversion and sorting) steps starting from\
   			filtering.

- •

  `"reference"` - path to/name of reference genome in fasta format (.fa)

### Optional

- •

  `"mismatch"` - number of mismatches to allow when filtering/removing the tag. Default = 0

- •

  `"tagdirection"` - direction of the tag, 5' or 3'. Default = 3

- •

  `"mapping_score"` - cutoff value for mapping score when creating insertion site plots. Default = 30

- •

  `"tag"` - TraDIS tag to filter and then remove

## METHODS

`"run_tradis"` - run complete analysis with given parameters

## AUTHOR

Carla Cummins \<path-help@sanger.ac.uk\>

## COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

```
  The GNU General Public License, Version 3, June 2007
```