Peter Briggs pjbriggs

@fls-bioinformatics-core

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pjbriggs / make_bw_files.sh

Created May 2, 2013 11:26

Utility script to create bigWig files from phastCons wig data files. Needs the chromosome sizes which can be obtained by doing e. "fetchChromSizes mm9 > mm9chromSizes". For each .data file in the specified directory, runs wigToBigWig to generate corresponding .bw file.

	#!/bin/sh
	#
	CHROMSIZE_FILE=$1
	if [ -z "$CHROMSIZE_FILE" ] ; then
	echo "Usage: $0 CHROMSIZE_FILE [ DATA_DIR ]"
	exit
	fi
	if [ -z "$2" ] ; then
	DATA_DIR=`pwd`
	else

pjbriggs / usage.sh

Created January 30, 2013 12:40

Report disk usage under specified directory (largest subdirectories and largest files)

	#!/bin/sh
	#
	# Report disk usage
	#
	# Usage: usage.sh DIR
	#
	if [ $# -eq 0 ] ; then
	echo "Usage: $0 DIR"
	exit
	fi

pjbriggs / report_barcodes.py

Created January 24, 2013 11:20

Count and report the index sequences (aka barcode tags) in an Illumina FASTQ file

	#!/bin/env python
	#
	# Count and report the barcode tags in a fastq file from Illumina
	# sequencing platform
	#
	import sys
	import FASTQFile
	fastq_file = sys.argv[1]
	tags = {}
	for read in FASTQFile.FastqIterator(fastq_file):

pjbriggs / make_nibs.sh

Created January 21, 2013 15:54

Example script for generating sequence alignment files (.nib) using faToNib submitted to a Grid Engine cluster

	#!/bin/sh
	#
	# make_nibs.sh
	#
	chroms=`ls chr*.fa`
	for chrom in $chroms; do
	echo $chrom
	nib=${chrom%.*}.nib
	qsub -cwd -V -b y faToNib $chrom $nib
	done

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