Results for "Awk"
Users
Skills: Awk2327 days ago
Blogs
- AWK is a standard tool on every P...scripting language. Why use AWK instead of Perl? Readability....There is an implied loop and AWK automatically reads and parse...articularly useful to prevent AWK from assuming the arguments...localvar, arr) { # AWK, being a string-processing la...
1835 days ago
Run bash script in Perl program !
...;my $in, 'command', 'arg1', 'arg2'); 5.a2p syntax: a2p [options] [awkscript] There is a Perl utility known as a2p which translates awk command to Perl. It takes awk...637 days ago
Bookmarks
Linux command line exercises for NGS data processing
...torial [uzi@quince-srv2 ~/linuxTutorial]$ I have deliberately chosen Awk in the exercises as it is a l...line tools such as grep, sed, perl etc. Furthermore, having a command on awk will make it easier to unders...2873 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
....fq reads.fq | gzip -1 > reads.paf.gz Then we can assemble miniasm -f reads.fq reads.paf.gz > reads.gfa Convert GFA to FASTA: awk '/^S/{print ">"$2"\n"$3}'...2350 days ago
Top-level pages
Most Commonly used Awk by Bioinformatician
...its functionality with Perl, awk is simpler in many practical cases. Why awk? You can replace a pipeline o...thing on the fly. You can use awk to make a neat one-liner for...}' input.txt > output.txt awk 'BEGIN{OFS="\t"}{print $2,$4,...ed is simpler in this case): awk '{sub(/test/, "no", $0);print...3912 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...BMC Bioinformatics 11(Suppl 12):S1, 2010 Full Text Links to Linux command-line tutorials and resources Tutorials for AWK, a powerful tool for handling data tables A set of awk notes from Boston University...3779 days ago
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Wire posts
Fun
- ...data! Why did the bioinformatician attend the gay pride parade? A: They supported polymorphism. Why did bioinformatician prefer awk, PerlOneliner? A: Because ev...
3180 days ago
Bio-Scripts
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2617 days ago
Download the genome from NCBI using bash script/command
...efseq/fungi/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...nk/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...seq/archaea/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...nvertebrate/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...2531 days ago
- +36 more Bio-Scripts
Groups
Awk is widely used these days for extracti...logical data in Unix/Linux.Most of the awk code is single liner. Useful...eblinks: http://www.grymoire.com/Unix/Awk.html http://www.hcs.harvard....t http://www.math.utah.edu/docs/info/gawk_5.html http://www.osnews.com...3919 days ago
Tags
- There are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the sequence header and sequence need...
Tags: fasta, fastq, convert, sed, awk, seqtk, bioawk, fastx, Emboss, fastq2fasta
2305 days ago
Most Commonly used Awk by Bioinformatician
Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases. Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single ...Tags: Awk, Bioinformatics
3912 days ago
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Comments
Comment on "Run miniasm assembler on nanopore reads !"
...1 > ./minimap.paf.gz miniasm -f \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfa awk ’/^S/{print “>...796 days ago
- ... awk [-off ...] [-F sep_re] [-v VA...p; Advanced feature filtering using awk syntax. &nbs...
1520 days ago
- +11 more Comments
