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.