Comment on "Run miniasm assembler on nanopore reads !"
...-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}' reads.gfa |...2189 days ago
Comment on "Perl one-liner for bioinformatician !!!"
...file to lowercase dd $ dd if=input.txt of=output.txt conv=lcase tr $ tr '[:upper:]' '[:lower:]' < input.txt > output.txt awk $ awk '{ print tolower($0) }' input.txt >...2228 days ago
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Comment on "Generating a random string with Perl"
Hmmm interesting, but I prefer Perl module String::Random; use String::Random;my $pass = String::Random->new;print "Your password is ", $pass->randpattern("CCcc!ccn"), "\n"; This would output something like this:Your password is UDwp$tj52921 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Rename the name of multi fasta sequesnces with awk awk '/^>/{print ">chromosome" ++i; next}{print}' < file.fasta2994 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
To deal with simple CSV: awk -F, '{print $1,$2}'3641 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Print line of a tab-delimited file when the 8th field is 10090:awk -F "\t" '$8 == 10090 { print $0 }' myFilePrint fields 1, 2, 3 from a tab-delimited file where the 4th field contains a '99':awk -F "\t" '$4 ~ /99/ {print $1"\t"$2"\t"$3}' myFile3723 days ago
Comment on "Bioinformatics Definitions"
What is Bioinformatics? A Proposed Definition and Overview of the Field http://archive.gersteinlab.org/papers/e-print/whatis-mim/text.pdf3835 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
To double space a file; $ awk '1; { print "" }' : To prints the number of words in a file; $ awk '{ total = total + NF }; END { print total+0 }' :3916 days ago