Create required files

Create construct.txt

In order to generate figures with construct information, you need to add that info. Create a txt-file with gene info per line, separated by space. The info should be; 1) name, 2) start position and 3) end position.

e.g.

Amp 1 500   
lyz 1000 1200       
Gene1 2000 5000		      
Gene2 7000 7700	     		

Make Configuration file

Create a configuration file from template.

$ cp TC_hunter/template/TC_hunter.config /path/to/WorkingDir 

Add required information to config file

TC_hunter.nf

Argument	Usage	Description
WorkingDir	<Path/WorkingDir>	Path to your working directory (this is where the output html and figures will be)
TC_hunter_path	<Path/TC_hunter>	Path to TC_hunter, only TC_hunter if it's in your $PATH
Construct_file	<Path/construct.txt>	Path to your construct.txt file (See construct file below)
Construct_length		The length of your construct in numbers
Construct_name		The name of the construct, most match the name in the reference file
bam	<Bam_directory>	The path to the directory where you have your bam file or (if several sampes) bam files.
Reference	<Jointref.fa>	Path to the merged reference file including both host and construct genome

e. g. example.config

TC_hunter_BWA.nf

Argument	Usage	Description
WorkingDir	<Path/WorkingDir>	Path to your working directory (this is where the output html and figures will be)
TC_hunter_path	<Path/TC_hunter>	Path to TC_hunter, only TC_hunter if it's in your $PATH
Construct_file	<Path/construct.txt>	Path to your construct.txt file (See construct file below)
Construct_length		Length in numbers of your construct that will be plotted
Construct_name		Name of the construct, most match the neme in your reference file
sample	<sample_directory>	Path to directory where you have the fastq-files (R1 and R2)
folder	<sample_directory>	Path to directory containing one directory for each sample. The name of the samples will be the same as the directory names
host_ref	<host_ref.fa>	Path to host reference file
construct_ref	<construct_ref.fa>	Path to construct reference file

e. g. example.config