3466 days ago
3536 days ago
Install ImageMagick from Unix Source
...te: Total 124593 (delta 94), reused 94 (delta 64), pack-reused 124452Receiving objects: 100%...ocessor... gcc -Echecking for a sed that does not truncate output...essor... g++ -Echecking for ld used by g++... /usr/bin/ld -m elf_...www/api/MagickWand/ftv2folderclosed.png /usr/local/share/doc/Imag...2188 days ago
Linux command line exercises for NGS data processing
...ial is to introduce students to the frequently used tools for NGS analysis as wel...exercises as it is a language in itself and is used more often to manipulate NGS...d to the other command line tools such as grep, sed, perl etc. Furthermore, havin...2916 days ago
2193 days ago
Most Commonly used Awk by Bioinformatician
...practical cases. Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call...input.txt deal with simple CSV: awk -F, '{print $1,$2}' substitution (sed is simpler in this case): aw...3954 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...mapping and assembly of GC-biased genomes. Kozarewa et al, Natu...TileQC: a system for tile-based quality control of Solexa dat...of high-throughput sequence-based experimental data. Carver et...ipting Guide Tutorials for sed, the command-line stream edit...3821 days ago
Download the genome from NCBI using bash script/command
...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...wk '{FS="\t"} !/^#/ {print $20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih...2574 days ago
Unzip all the genome file and remove all fasta header except first one
...f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print $0} ' $f | sed '/^>/{s/ /_/g}' > $f.fa #then sed '1!{/^\>/d;}' $f > $f.fa...2573 days ago
Comment on "Perl one-liner for bioinformatician !!!"
...nput.txt > output.txt awk $ awk '{ print tolower($0) }' input.txt > output.txt perl $ perl -pe '$_= lc($_)' input.txt > output.txt sed $ sed -e 's/\(.*\)/\L\1/' input.txt...2256 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Aakhsyan webpage explain commonly used sed and awk for bioinformatics at http://raunakms.wordpress.com/2013/06/08/sed-and-awk-for-bioinformatics/...3950 days ago