BOL

Decontamination https://img.jgi.doe.gov/er/doc/SingleCellDataDecontamination.pdf #Bacteria #Contamination

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

Perl OneLiner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #Oneliner #NGS #Script

NGS onliner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsetFASTAFASTAQ.html #OneLiner #NGS

splitbed to splitcov https://github.com/cyaguesa/Rscripts/blob/master/splitbed_to_splitcov.R #R #Coverage

Meta-genomics assembly http://denbi-metagenomics-workshop.readthedocs.io/en/latest/index.html #Genomics #Meta #Assembly #Bacteria #Workshop #Tutorial

Learn Biostats http://www.who.int/ihr/lyon/surveillance/biostatistics/en/ #BioStat #Learn #CD

To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta

To add something to end of all header lines: $ sed 's/>.*/&WHATEVERYOUWANT/' file.fa > outfile.fa #Add #Fasta

use File::Basename; use lib dirname (__FILE__); # To search lib in local folder #Perl #Modules

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

How to calculate the #Euclidean and #Manhattan distance? http://math.stackexchange.com/questions/139600/how-to-calculate-the-euclidean-and-manhattan-distance

Sample README git file https://gist.github.com/PurpleBooth/109311bb0361f32d87a2 #Git #Readme #Create #GitHub