Thomas Sandmann tomsing1

Download the following two BED files from the RSEQC website, hosted on SourceForge:

hg38_RefSeq.bed.gz: All human RefSeq transcripts
hg38.HouseKeepingGenes.bed.gz: Subset of human RefSeq transcripts considered housekeeping genes

Extract the RefSeq identifiers from the HouseKeepingGenes file.
Map the RefSeq identifiers to orthologous genes in your species of interest, e.g. using ensembl's BioMart web interface. Make sure the return the gene stable ID for the target species.

Installing Nextflow on a Mac

 brew install adoptopenjdk8

Install Nextflow: curl https://get.nextflow.io | bash in the current directory
Optional: Move the nextflow binary to a directory that is in the PATH.

	libraries = c("zellkonverter", "SingleCellExperiment")
	for (lib in libraries) {
	suppressPackageStartupMessages(library(lib, character.only = TRUE,
	quietly = TRUE))
	}

	# dummy SingleCellExperiment
	ncells <- 100
	u <- matrix(rpois(20000, 5), ncol = ncells)
	v <- log2(u + 1)

	libraries = c("basilisk", "mypackage", "zellkonverter",
	"SingleCellExperiment")
	for (lib in libraries) {
	suppressPackageStartupMessages(library(lib, character.only = TRUE,
	quietly = TRUE))
	}

	# create dummy SingleCellExperiment
	ncells <- 100
	u <- matrix(rpois(20000, 5), ncol = ncells)

	#!/usr/bin/env bash

	set -e
	set -x
	set -o pipefail

	# This bash script retrieves SRA archives for a runs listed in the
	# SRR_Acc_List.txt file (available from the SRA Run Selector).
	#
	# It requires:

	#!/usr/bin/env bash

	set -e
	set -x
	set -o pipefail

	declare -r CORES=$(getconf _NPROCESSORS_ONLN)
	declare -r REFERENCE="s3://your-reference-bucket/gencode/release_30/GRCh38_p12/"
	declare -r S3_FASTQ="s3://your-bucket/Fastq/"
	declare -r MIN_OVERLAP=10 # the larger the better

	#' Centered log-ratio transformation
	#'
	#' @param m Count matrix with features in rows and samples (cells) in columns
	#' @return matrix
	#' @export
	clr <- function(m) {
	apply(m, 2, function(x) {
	log1p(x = x/(exp(x = sum(log1p(x = x[x > 0]), na.rm = TRUE)/length(x = x))))
	})
	}

	# Shell function to subsample to a fixed number of alignments,
	# requiring the sambamba and samtools suites to be available.
	# see https://www.biostars.org/p/76791/
	function SubSample {
	local FACTOR=$(samtools idxstats $1 \| cut -f3 \| \
	awk -v COUNT=$2 'BEGIN {total=0} {total += $1} END {print COUNT/total}')

	if [[ $FACTOR > 1 ]]
	then
	echo '[ERROR]: Requested number of reads exceeds total read count in' $1 '-- exiting' && exit 1

	"""Filter alignments based on R1 and R2 start positions

	Example: python extract_alignments.py example.bam filtered.bam
	"""

	import argparse
	import sys
	from pysam import AlignmentFile

	parser = argparse.ArgumentParser()

	#!/usr/bin/env bash

	# This script provisions an EC2 instance via docker-machine and takes the
	# following positional arguments
	# 1. docker-machine name (bioinfo-sandmann)
	# 2. login username (ubuntu)

	set -e # exit upon error
	set -o nounset # no unset variables