nuada’s gists

nuada / refdiff.sh

Last active August 29, 2015 13:56

Compare regions of reference sequences

	#!/bin/bash
	# usage: refdiff.sh <h37>.bed <hg19>.bed

	bedtools getfasta -fi /resources/h37/human_g1k_v37.fasta -bed $1 -fo - \| sed -e 's/MT/M/' \| tr '[:lower:]' '[:upper:]' > tmp.h37.fasta
	bedtools getfasta -fi /resources/hg19/ucsc.hg19.fasta -bed $2 -fo - \| sed -e 's/chr//' \| tr '[:lower:]' '[:upper:]' > tmp.hg19.fasta
	diff -u tmp.h*.fasta
	rm tmp.h*.fasta

nuada / r_setup.sh

Last active January 8, 2016 10:52

	#!/bin/bash

	source /etc/lsb-release
	echo "deb http://r.meteo.uni.wroc.pl/bin/linux/ubuntu ${DISTRIB_CODENAME}/" > /etc/apt/sources.list.d/cran.list
	apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

	apt-get update
	apt-get upgrade -y
	apt-get install -y r-cran-dbi libcurl4-openssl-dev libxml2-dev libjpeg62

nuada / bioc_exparrays.R

Last active August 29, 2015 13:57

	source("http://bioconductor.org/biocLite.R")
	biocLite()
	biocLite('AnnotationForge')
	biocLite(c('illuminaio', 'beadarray', 'minfi', 'minfiData', 'limma', 'ChAMP', 'ChAMPdata'))
	biocLite('IlluminaDataTestFiles')

nuada / download_blast_db.sh

Created March 31, 2014 12:13

	#!/bin/bash
	#usage: $0 <prefix> <number of parts>
	#eg: $0 nt 17

	# Download blast db form NCBI
	for i in $(seq -f '%02.f' 0 $2); do
	wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/${1}.${i}.tar.gz
	wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/${1}.${i}.tar.gz.md5
	done

nuada / blast_unassigned_otus.sh

Created April 1, 2014 09:34

Parallel blasting of bacterial sequences, inspired by: http://students.washington.edu/bowmanjs/wordpress/?p=737

	#!/bin/bash

	number_of_jobs=4
	# Opts for fast blasting, http://www.biostars.org/p/16425/#16431

nuada / r_bicg_prerequisites.R

Last active August 29, 2015 14:01

	source("http://bioconductor.org/biocLite.R")
	biocLite();
	biocLite("aCGH");
	source("http://aroma-project.org/hbLite.R");
	hbInstall("aroma.affymetrix");
	install.packages("ggplot2")
	install.packages("gplots")

nuada / hydra2bed.sh

Last active August 29, 2015 14:01

	#!/bin/bash

	echo "track name=\"$(basename $1)\" description=\"hydra output\" useScore=0 colorByStrand=255,0,0 0,0,255 gffTags=on"
	awk -F '\t' '{ \
	gsub("+", "forward", $9); \
	gsub("-", "reverse", $9); \
	print $1 FS $2 FS $3 FS "Name=" $7 ";Strand=" $9 ";numMapping=" $16 FS FS $9; }' $1
	awk -F '\t' '{
	gsub("+", "forward", $10); \
	gsub("-", "reverse", $10); \

nuada / ab2bam.sh

Last active May 8, 2022 02:27

Convert ab1 sanger sequencing traces to fastq and align them to reference

nuada / bed2reg

Last active August 29, 2015 14:02

Convert BED file to PLINK/SEQ REG format

	#!/bin/bash

	echo -e "#CHR\tBP1\tBP2\tID"
	awk -F '\t' '{ print $1 FS $2+1 FS $3 FS NR }' \| sed -e 's/^$[0-9]\+$/chr\1/g'

nuada / bed_cleanup.sh

Last active August 29, 2015 14:02

Cleanup BED: sort and merge intervals, extract gene symbols

bedtools sort -i foo.bed | bedtools merge -i - -nms | sed -e 's/\r//g' | awk -F '\t' '{ split($4, name, "."); print $1 FS $2 FS $3 FS name[1] }'

Piotr Radkowski nuada