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http://www.nbcnews.com/health/health-news/boys-mysterious-infection-cured-after-dna-sequencing-n122871 #HealthOmics

Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName #Delete #Space #Fasta #Perl #Oneliner

Remove N from a fasta file. Go to vi editor, type :%s/N\{25,\}//g and press enter. #Vim #vi #N #Replace #Fasta

perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta

rename all *.txt as *.bak: find . -name "*.txt" | sed "s/\.txt$//" | xargs -i echo mv {}.txt {}.bak | sh #Linux #Rename #Oneliner

There are several other softwares Eland: http://illumina.ucr.edu/illumina_docs/Velvet:http://www.ebi.ac.uk/~zerbino/velvet/Maq (Mapping and Assembly with Quality): http://maq.sourceforge.net/maq-man.shtmlSOAP alignment tool:...

Force install a Perl module sudo PERL_MM_USE_DEFAULT=1 perl -MCPAN -e "CPAN::Shell->force(qw(install Nginx::Log::Entry))" #Perl #Install #Force #CPAN #Module

R package SPP for chip-seq analysis. It can read quite a few aligner's output file. Here is the original package tutorial. http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.htmlHere is my version of the...

Use multi-core with Perl programs http://perltricks.com/article/61/2014/1/21/Make-your-code-run-faster-with-Perl-s-secret-turbo-module #Perl #MCE #Speed #Module

Generate map with R http://students.washington.edu/bowmanjs/wordpress/?p=1003