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NGS analysis pipeline http://www.egr.msu.edu/changroup/Protocols/NGS%20analysis%20example%20of%20a%20pipeline.html #Pipeline #NGS #Genomics #Tutorial

We generally receive some common question like ... where to find human reference genome? What is reference annotation, how to download it etc. Here are some resources that I found...

FDA Applies Genome Sequencing !! http://www.foodsafetynews.com/2014/06/fda-applies-genome-sequencing-in-outbreak-investigation/#.U5G5zvmSych #FoodOmics

Small RNA Determines Sex !! http://www.biotechniques.com/news/Small-RNA-Determines-Sex/biotechniques-352151.html#.U5G2tPmSycg #RNaOmics #piRNA

Sheep genome decoded!! http://www.sciencemag.org/content/344/6188/1168.abstract #Omics #Seq

Genetic sequencing traced root of MERS!! http://time.com/2827822/it-looks-like-camels-actually-can-transmit-mers-to-humans/ #HealthOmics

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