Monday, May 15, 2017

Jackson lab genomics Day 1


install anaconda3 on ubuntu virtualbox

hqin@rainboxdash:~/anaconda3/bin/$ ./jupter notebook & 

samtools view example.bam | less

Linux exercises: up and down arrows, tab for file-names autocomplete

bam file

vcf file (variant call file?)

less test.vcf

mkdir tmpdir
cd tmpdir
cd ..

Essential probability and statistics for introduction to big data

  • summary stattistics vs empirical statistics
  • Common data transformation, Z-scores
  • Bayesian inference
  • Multiple hypothesis testing

Bayes's rule

Introductory Data Mining


 all biology are computational
 computational biology are parasite of biology

  research project approach using real datasets
  targeted students: professional and academic oriented?

data carpentry's R for genomcis

RStudio projects


Barke Southern Illinois Medical School, longest-living mouse

Brenton Gravely, RNA genomics

Dscam, over 100 exons, an extreme case of alternative splicing
Schmucker 2000 Cell. Mutually exclusive splicing.
Ig Repeats.  Dimerization are isoform specific.

Dscam variatiosn between species
Gravely 2005, Cell.

Competing RNA base-pairing is a common mechanism for mutually exclusive splicing in anthropods, Yang 2011 Nature Struc Mol Biol

single cell RNA sequencing
Drosophila S2 cells, each cell show the same splicing isoform.

Drop-seq of Drosophila and human cell to control the number of cells in each droplet.

Oxford nanopore sequencing

1500 RNA binding proteins in human genome

Van Nostrand Nature methods, 2016, eCLIP-seq reveqls RBP-specific binding profiles

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