Pseudomonas Nullarbor Step-by-step

Here are the basic steps for doing the Pseudomonas analysis using Nullarbor.

By Emily Richardson.

# make project directory 

mkdir 2016_10_21_Pseud
cd 2016_10_21_Pseud

#click on view project xml

#Select the link for the reads,fastq_ftp,fastq_md5,fastq_bytes

#edit this link to only request submitted_field

#Change name to somthing more meanginful

mv filereport\?accession=PRJEB6515\&result=read_run\&fields=submitted_ftp.1 read_locations.txt

# replace the semi colon with a new line

tr ';' '\n' < read_locations.txt > reads.txt

# get the subset you require from 
wget ""

# get the subset from reads.txt
 grep -f cc17_subset.txt reads.txt > cc17_reads.txt

download these reads
wget -i cc17_reads.txt

# make directory for your reads
mkdir reads

#move all reads to reads folder
mv *gz reads

# get the reference PAO1 Pseduomonas Aeruginosa

# This is the command to make your nullarbor input file 

cd reads
for read1 in *R1*gz ; do printf "${read1%_R1*}\treads/${read1}\treads/${read1%_R1*}_R2_paired.fastq.gz\n" ; done > ../

cd ../ --name cc17_pseud --mlst paeruginosa --ref NC_002516.gbk --input --outdir cc17_pseud_nullarbor
 nice make -j 1 -C /home/ubuntu/2016_10_21_Pseud/cc17_pseud_nullarbor
# Run nullarbour MAKE SURE YOU ARE IN A SCREEN!!!