code_for_testing.txt

# For raj lab, this is how probes were generated
# cd into the test_target folder then run (wanted 50 oligos):

mkdir raj_output

mkdir raj_output/unformat
mkdir raj_output/formatted


for i in *fa; do python ../Raj_lab/ProbeDesign/DesignServer/find_probes_cl.py $i probe 50 > raj_output/unformat/${i}_raj.fa;tail -100 raj_output/unfor
mat/${i}_raj.fa > raj_output/formatted/${i}_raj.fa;done

# Had to modify the code a bit to remove other print statements

###############################
# Then for oligominer

mkdir oligominer_output/

mkdir oligominer_output/blocked

# Using 0% formamide and 1M Na+, probe size 20 and minimum Tm 40 with max Tm 80

for i in *fa; do python ../OligoMiner/blockParse.py -l 20 -L 20 -t 40 -T 80 -X AAAAA,TTTTT,CCCC,GGGG -F 0 -s 1000 -f $i;done

mv *fastq oligominer_output/blocked

cd blocked

# can't use this since the score min isn't low enough
# for i in *fastq; do bowtie2 -x /mnt/g/Research/Genome/hg38/hg38.bt2_index -U $i --no-hd -t -k 100 --very-sensitive-local -S ${i}.sam;done

for i in *fastq; do bowtie2 -x /mnt/g/Research/Genome/hg38/hg38.bt2_index -U $i --no-hd -t -k 2 --local -D 20 -R 3 -N 1 -L 20 -i C,4 --score-min G,1,4 -S ${i}.sam;done

mkdir ../aligned
mv *sam ../aligned
cd ../aligned

# cleaned sam output to bed
for i in *sam; do python ../../../OligoMiner/outputClean.py -T 42 -f ${i};done

mkdir ../cleaned
mv *bed ../cleaned/
cd ../cleaned

# making the jellyfish mer-file
# took a long time, file is huge
jellyfish count -m 18 -s 3G --bf-size 50G -t 24 /mnt/g/Research/Genome/hg38/hg38.fa

# Then checked for n-mers (18)
for i in *bed; do python ../../../OligoMiner/kmerFilter.py -f ${i} -m 18 -j ../mer_counts.jf -k 4; done
# took 1 minute each!

mkdir ../18_4_nmer_clean
mv *18_4.bed ../18_4_nmer_clean/
cd ../18_4_nmer_clean/

# make reverse complement which is the actual probe

for i in *bed; do python ../../../OligoMiner/probeRC.py -f $i;done
mkdir ../rc_probes
mv *RC.bed ../rc_probes/