Lukas leiendeckerlu

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.

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

	## RNA-seq analysis with DESeq2
	## Stephen Turner, @genetics_blog

	# RNA-seq data from GSE52202
	# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
	# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

	# Import & pre-process ----------------------------------------------------

	# Import data from featureCounts

	#!/bin/bash
	#
	# Author: Sean Davis <[email protected]>
	#
	# Uses named pipes (FIFO) to reduce storage needs
	# to call varscan somatic
	# Some details may need to be edited to meet particular needs
	# call with the following parameters
	# 1) The FASTA file containing the reference genome
	# 2) The Normal bam file