cbergman

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

cbergman

# download R: https://cran.rstudio.com/
# download Rstudio: https://www.rstudio.com/products/rstudio/download/


### Brief intro to R language ###
# R is a FOSS statistical programming language
# R is an implementation of S (Bell labs, 1976) by Ross Ihaka and Robert Gentleman (1995->2000)
# R name is play on S language and author names
# R is an interpreted language, R command line interpreter (console) is written in R, C and Fortran
# R interpreter takes plain text input, interprets input, and generates numerical, text or graphical output

cbergman

- Skelley et al 2013:
  - paper: http://genome.cshlp.org/content/23/9/1496.long
  - ena: http://www.ebi.ac.uk/ena/data/view/SRP018005 (includes RNA-seq)
  - 22 diverse Scer strains
  
- Bergstrom et al 2014
  - paper: https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu037
  - SGRP2 
  - 19 Scer
  - 22 Spar

cbergman

http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0001/Analysis_Results/m130605_000141_42207_c100515142550000001823076608221372_s1_p0.1.bax.h5
http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0001/Analysis_Results/m130605_000141_42207_c100515142550000001823076608221372_s1_p0.2.bax.h5
http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0001/Analysis_Results/m130605_000141_42207_c100515142550000001823076608221372_s1_p0.3.bax.h5
http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0001/Analysis_Results/m130605_000141_42207_c100515142550000001823076608221372_s1_p0.bas.h5
http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0001/m130605_000141_42207_c100515142550000001823076608221372_s1_p0.metadata.xml
http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0002/Analysis_Results/m130605_032054_42207_c100515142550000001823076608221373_s1_p0.1.bax.h5
http://datasets.pacb.com.s3.amazonaws.com/2013/Yeast/0002/Analysis_Results/m130605_032054_42207_c100515142550000001823076608221373_s1_p0.2.bax.h5
http://datasets.p

cbergman

#!/bin/bash

cd ../example/yeast/output/local/

for l in 100; do
  for o in 0; do
    for s in 0.02; do
      for i in 0; do
        for d in 0; do

cbergman

#!/bin/bash

cd ../example/ecoli/output/local/

for l in 100; do
  for o in 0; do
    for s in 0.02; do
      for i in 0; do
        for d in 0; do

cbergman

#!/usr/bin/env python
import sys

i = 0
ovlpstr = ''
ovlpln = 10  #20 , 2 for test
chnkln = 100 #200, 5 for test
start = 0
end = 0
chr = ''

cbergman

sudo apt-get install python-yaml
sudo apt-get install git
wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
python bcbio_nextgen_install.py install_directory data_directory > bcbio_install_output_log

cbergman

# Follow steps 1-4 on Ubuntu or 2-4 on Biolinux

1. Add repositories to your machine configuration

a. Bio-Linux
$ sudo add-apt-repository “deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux”
$ sudo apt-get update
$ sudo apt-get install bio-linux-keyring

b. CRAN