Provided by: bio-tradis_1.3.3+dfsg-3_all
NAME
bacteria_tradis - bio-tradis: run a TraDIS analysis
SYNOPSIS
bacteria_tradis [options]
DESCRIPTION
Run a TraDIS analysis. This involves: 1: filtering the data with tags matching that passed via -t option 2: removing the tags from the sequences 3: mapping 4: creating an insertion site plot 5: creating a stats summary
OPTIONS
-f text file listing fastq files with tradis tags attached -t tag to search for -r reference genome in fasta format (.fa) -td tag direction - 3 or 5 (optional. default = 3) -mm number of mismatches allowed when matching tag (optional. default = 0) -m mapping quality cutoff score (optional. default = 30) --smalt_k custom k-mer value for SMALT mapping (optional) --smalt_s custom step size for SMALT mapping (optional) --smalt_y custom y parameter for SMALT (optional. default = 0.96) --smalt_r custom r parameter for SMALT (optional. default = -1) -n number of threads to use for SMALT and samtools sort (optional. default = 1) -e set defaults for essentiality experiment (smalt_r = 0, -m = 0) -v verbose debugging output
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.