---
name: "tradis_gene_insert_sites"
section: "1"
platform: "linux"
package: "bio-tradis"
version: "1.4.1+dfsg-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/tradis_gene_insert_sites"
---

# tradis\_gene\_insert\_sites(1)

bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file

## NAME

tradis\_gene\_insert\_sites - bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file

## SYNOPSIS

**tradis\_gene\_insert\_sites**

## DESCRIPTION

Take in a plot file(s) and an embl file and produce a tab delimited file with insert site details to use as input to an R script to t est for essentiality.

- **-o**\|output\_suffix

  \<suffix to add to output files (optional, default = tradis\_gene\_insert\_sites.csv)\>

- **-trim5**

  \<trim insertion sites from 5' end of gene (optional, default = 0)\>

- **-trim3**

  \<trim insertion sites from 3' end of gene (optional, default = 0)\>

- **-j**\|joined\_output

  \<output a single file with all info. default = one file per input file\>

- **-h**\|help

  display this message

## EXAMPLES

-

  tradis\_gene\_insert\_sites my\_annotation.embl my\_insert\_site\_plot.gz

-

  tradis\_gene\_insert\_sites my\_annotation.embl my\_insert\_site\_plot

- \# multiple plot files

  tradis\_gene\_insert\_sites my\_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz

- \# specify an output suffix this will result in a file named my\_insert\_site\_plot1.my\_output.csv

  tradis\_gene\_insert\_sites **-o** my\_output.csv my\_annotation.embl my\_insert\_site\_plot1

- \# Trim insertion sites from start or end of gene

  tradis\_gene\_insert\_sites my\_annotation.embl **-trim5** 0.1 **-trim3** 0.1 my\_annotation.embl my\_insert\_site\_plot.gz

The trim parameter is the fraction of the gene length trimmed.

- \# place all info into a single file

  tradis\_gene\_insert\_sites **-o** output\_suffix.csv **-j** my\_annotation.embl plot1.gz plot2.gz plot3.gz

Resulting file: joined\_output.output\_suffix.csv

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.