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Chi squared test https://edwards.sdsu.edu/research/calculating-chi-squared-wiht-perl/ #Perl #Chi #Probability

Data structure with R http://staff.washington.edu/jon/dsa-perl/dsa-perl.html #R #Data #Structure #Script #Perl

Interesting PPT on cancer genomics https://www.genome.gov/multimedia/slides/genomicsinmedicine2013-2014/helman_6-7-2013.pdf

BioStats with R https://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf #R #BioStats #Example

Online free programming books https://github.com/vhf/free-programming-books/blob/master/free-programming-books.md

Essential perl http://cslibrary.stanford.edu/108/EssentialPerl.html

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

Check out the OS type: $ cat /etc/*-release #Linuxv #OS

Extract values : cat seeALN.xls | grep -w "scaffold_1" to #grep #exact #matching words from file seeALN.xls

Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa #Length #Linux #OneLiner

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

Slice on the fly with perl: my ($username, $real_name) = (split /:/, $str)[0, 4]; #Perl #PerlTrick #Split

Re-install perl in Ubuntu: sudo aptitude reinstall perl #Perl #Ubuntu #Install #Linux

Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

Coverage R Plot http://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Genome #Image #NGS #BAM