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bacteria_tradis - bio-tradis: run a TraDIS analysis

BACTERIA_TRADIS(1) User Commands BACTERIA_TRADIS(1)

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.
March 2017 bacteria_tradis 1.3.1