bacteria_tradis1

Usage

Overview

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