UNIX and NGS
praha-january-2016
Installation instructions
Connecting to the virtual machine
Unix - Basics
Unix - Advanced I
Unix - Advanced II
Graphics session
Read quality
Genome assembly
Genomic tools session
Variant quality
Links
Bash
R Studio
Visual design
Genomic tools
Genomic data formats
Best practice
Reference manual for UNIX introduction
Important NGS formats
Additional exercises
Course materials preparation
Slide decks
UNIX and NGS
Docs
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Links
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Links
¶
Here is few sources that you can go through, when you get bored during the course...
Bash
¶
http://www.tldp.org/LDP/abs/html/
http://www.catonmat.net/blog/bash-one-liners-explained-part-three/
http://wiki.bash-hackers.org/howto/redirection_tutorial
http://wiki.bash-hackers.org/scripting/bashchanges
R Studio
¶
http://www.rstudio.com/resources/cheatsheets/
Visual design
¶
one secret link you got by email
http://www.smashingmagazine.com/2014/03/28/design-principles-visual-perception-and-the-principles-of-gestalt/
http://www.vanseodesign.com/web-design/gestalt-principles-of-perception/
http://colorbrewer2.org
Genomic tools
¶
http://bedtools.readthedocs.org/en/
http://bedops.readthedocs.org/en/
http://vcftools.sourceforge.net
Genomic data formats
¶
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40
http://www.ensembl.org/info/website/upload/gff.html
https://genome.ucsc.edu/FAQ/FAQformat.html#format1
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