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Nano tricks https://wiki.gentoo.org/wiki/Nano/Basics_Guide #Nano #Tricks

Show before(B) and after(A) the matching region $ grep -B 3 -A 2 foo README.txt #Linux #Tricks #View #Grep

Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner

Accept file from STDIN in Perl my $infh = \*STDIN; my $outfh = \*STDOUT #Perl #Tricks

Extract ten lines below matched string with grep: grep -A 10 "string" filename1 ; -B for above and -C for both #grep #Linux #Tricks #Lines #Matches

Split the text file with line number in Linux: wc -l abc.txt and then: split -l 60000 abc.txt #Split #Break #Line #Ubuntu #Linux #Tricks

Little correction, I guess you mean concatenate many files: $ for a in *.txt ; do cat $a >> newFile ; done #Linux #Tricks

Contact many files: $ for a in *.txt ; do cat $a >> newFile ; done #Linux #Tricks

Find a file with certain size and delete them: $ find . -name "see-D-d-ALN_*" -size -10k -delete #Delete #Size #Linux #Tricks

du -sh * will give you the size of all the directories,files etc in current directory in human readable format. #Linux #Size #Tricks #Folders #Files

Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS

Perl Elements to Avoid http://perl-begin.org/tutorials/bad-elements/ #Perl #Tricks #Avoid #Learn #Beginners

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

Get line number with Perl $fh->input_line_number() #Perl #Tipsoftheday #Tricks

Bacterial genome assembly tips using Valvet http://pathogenomics.bham.ac.uk/blog/2009/09/tips-for-de-novo-bacterial-genome-assembly/ #Assembly #NGS #Bacteria #Genome #Tricks #Tips #Velvet