Results for "sed"
Users
Interests: Polymeric scaffold based optoelectronic materials3409 days ago
- About me: ...-aided drug/vaccine design (probably highest number of services developed/maintained from a single group in the world). These services are heavily used by scientific community, near...
3479 days ago
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Blogs
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...2130 days ago
Bookmarks
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...2859 days ago
Files
- ...wa_aln_core] 70778880 sequences have been processed.[bwa_aln_core] calculate SA c...wa_aln_core] 70989574 sequences have been processed.[main] Version: 0.7.15-r1140[...G_v2.0.6/all_p_ctg.fa | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > FALCON-Unzip-...
2136 days ago
Top-level pages
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...3897 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...3764 days ago
- +5 more Top-level pages
Wire posts
Bio-Scripts
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...2516 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...2515 days ago
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Tags
Awk is widely used these days for extraction and manipulation of large scale biological data in Unix/Linux.Most of the awk code is single liner. Useful Weblinks: http://www.grymoire.com/Unix/Awk.html http://www.hcs.harvard.edu/~dholland/computers/awk.html http://www.pement.org/awk/awk1line.tx...Tags: awk, gawk, nawk, sed, data, sequencing, one liner
3904 days ago
Tags: awk, merge, sed, gawk, nawk
3498 days ago
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Comments
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...2198 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/...3892 days ago
