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. |
# 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 |
- 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 |
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 |
#!/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 |
#!/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 |
#!/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 = '' |
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 |
# 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 |