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
vcf file (variant call file?)
Essential probability and statistics for introduction to big data
- summary stattistics vs empirical statistics
- Common data transformation, Z-scores
- Bayesian inference
- Multiple hypothesis testing
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
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