Ismail Moghul IsmailM

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.

This issue is so infuriating that I'm going to take some time to write about it.

MOST IMPORTANT. Your local development server must be bound to IP address 0.0.0.0. Some do this by default, but many don't. You need to make sure that you run your local server with correct IP bindings. You may need to provide additional flags to your serve commands e.g. polymer serve --hostname domain.local, hugo serve --bind 0.0.0.0. If you use a named domain like domain.local, it has to be defined in /etc/hosts and pointing at 0.0.0.0.
My Parallels setting is using Shared Network, nothing special there.
Open macOS Terminal and type ifconfig. Look for the value under vnic0 > inet. It is typically 10.211.55.2.

As configured in my dotfiles.

start new:

tmux

start new with session name:

	/*
	* -------------------------------------------------
	* Base Nextflow config file
	* -------------------------------------------------
	* This file contains basic process requirement setup
	* It DOES NOT contain any config for cluster, so will run
	* in default mode by itself. It should be used with
	* the max_memory, max_cpus and max_time params for
	* customising hardware limits
	*/

	# Folder setup

	# contains reference indexes
	ref_indexes:
	dbsnp.index ref_indexes/hg38.BS.gem ref_indexes/hg38.BS.info ref_indexes/hg38.contig.sizes

	fastq:
	- GM12878_1:
	- GM12878_1_1.fastq.gz
	- GM12878_1_2.fastq.gz

	---
	destination:
	type: library
	name: 'PGP-UK Open Access Data'
	description: 'Open Access Genomic, Transcriptomic and Methylomic Data from the Personal
	Genome Project UK. DOI: 10.1186/s12920-018-0423-1'
	items:
	- name: Genetic Data (WGS)
	description: Open access WGS data from the PGP-UK Project
	items:

	#!/bin/bash

	[ $# -eq 0 ] && { echo "Usage: $0 SAMPLE_NAME"; exit 1; }

	set -ex

	export THEANO_FLAGS='device=cuda,floatX=float32'
	export CPLUS_INCLUDE_PATH=/usr/local/cuda-10.1/include
	export KERAS_BACKEND=theano
	ROOT_DIR=/home/ucbtmog/deepcpg

	# Download PGP Data CSV
	# Contains three columns:
	# - PGP-UK Hex ID
	# - Direct Link
	# - Type of Data
	wget https://www.personalgenomes.org.uk/data/data_file_links.csv

	# Here we display the Types of Data that are available
	cat data_file_links.csv \| cut -d ',' -f 3 \| sort \| uniq -c

	#!/bin/sh

	if [ "$1" == "" ]; then
	echo "Usage: $0 <folder to compress>"
	exit
	fi

	NAME=`basename $1`

	tar -c --use-compress-program=pigz -f $NAME.tar.gz $NAME

	# install.packages('data.table')
	# install.packages('ggplot2')
	# install.packages('GenomicRanges')
	library('data.table')
	library('ggplot2')
	library(GenomicRanges)

	# OUTPUT from GEMBS
	read_filtered_cpg_file <- function(file, project_title) {
	header <- c('contig', 'position', 'reference.genotype', 'called.genotype', 'genotype.score',