Results for "One-liner"
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Perl one-liner for beginners !
...;' columnFileWithTabs.txt > justSecondColumn.txt One-Liner: Sort lines by their length...rt {length $a <=> length $b} <>' textFile One-Liner: Print second column, unless...1380 days ago
Bookmarks
Download mutliple fasta file from NCBI in one GO!!
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...3909 days ago
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- 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,...
3267 days ago
Top-level pages
Most Commonly used Awk by Bioinformatician
...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...3911 days ago
Perl one-liner for bioinformatician !!!
...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...3627 days ago
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Bio-Scripts
- 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
1832 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### converting...1601 days ago
- +3 more Bio-Scripts
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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:...3918 days ago
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Perl one-liner for bioinformatician !!!
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.),...Tags: Bioinformatics, Computational Biology, Perl, NGS, Genome, Hacking, One-liner, Oneliner
3627 days ago
Comments
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
Check the perl module Test if dependencies are met by running this perl one-liner: perl -e "use JSON::XS;"1233 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Some of the commonly used bioinformatics one-liner by Stephen Turner @ https://github.com/stephenturner/oneliners3809 days ago
