BOL: Results for "One-liner"

Perl one-liner for beginners !

Fri, 24 Jul 2020 05:58:28 -0500

...;' columnFileWithTabs.txt > justSecondColumn.txt One-Liner: Sort lines by their length...rt {length $a <=> length $b} <>' textFile One-Liner: Print second column, unless...

Download mutliple fasta file from NCBI in one GO!!

Wed, 21 Aug 2013 08:13:30 -0500

if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs o...

Perl One liner basics !!

Sun, 24 May 2015 09:28:33 -0500

Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e,...

Most Commonly used Awk by Bioinformatician

Mon, 19 Aug 2013 01:12:38 -0500

...want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the ter....html http://www.grymoire.com/Unix/Awk.html A famous list of useful one-liners - though they're short, many...

Perl one-liner for bioinformatician !!!

Fri, 30 May 2014 05:49:07 -0500

...of Perl onliner is extremely helpful. Perl one-liners are small and awesome Perl p...bunch of files at once, and many more. Perl one-liners will make you the shell warr...gspot.com/2013/08/a-selection-of-useful-bash-one-liners.html http://biowize.wordpre...

Wire post by Abhimanyu Singh

Sat, 12 Jul 2014 15:09:10 -0500

Linux one-liner. https://wikis.utexas.edu/display/bioiteam/Scott%27s+list+of+linux+one-liners #Linux #Oneliner #NGS

Wire post by Rahul Nayak

Fri, 03 Jul 2015 01:50:13 -0500

Fancy One-Liner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #OneLiner #Bioinformatics #Quick #Common #Tricks #CommandLine #Terminal

One liner for reads mapping !

Sun, 28 Apr 2019 12:37:57 -0500

bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam

Samtools commands for bioinformatician !

Sun, 15 Dec 2019 10:31:22 -0600

## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### converting...

Perl one-liner for bioinformatician !!!

Fri, 30 May 2014 05:49:07 -0500

With the emergence of NGS technologies, and sequencing data most of the bioinformaticians mung and wrangle around massive amounts of genomics text. There are several "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.),...

Comment on "How to install Perl modules manually, using CPAN command, and other quick ways" by Neel

Thu, 17 Dec 2020 22:29:02 -0600

Check the perl module Test if dependencies are met by running this perl one-liner: perl -e "use JSON::XS;"

Comment on "Most Commonly used Awk by Bioinformatician" by Archana Malhotra

Thu, 28 Nov 2013 18:44:02 -0600

Some of the commonly used bioinformatics one-liner by Stephen Turner @ https://github.com/stephenturner/oneliners