Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip...1365 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp m...1365 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta...1357 days ago
Bash online to update Linux OS
sudo bash -c 'for i in update {,full-,dist-}upgrade auto{remove,clean}; do apt-get $i -y; done'691 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...NOT OK!\n }; #exit 1; } # end 'if' else { print "\n Module $_ OK!\n";} } # end 'for' } # end 'BEGIN' block #Bash script else here print "\n...1160 days ago
1158 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name dpkg -s $name &> /dev/null...1046 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my_file do filename=$(basename "$my_file") basename=...1045 days ago
962 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D961 days ago