nuada

#!/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

#!/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

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

nuada

#!/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

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

nuada

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

#!/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

#!/bin/bash                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                  
# Unzip files                                                                                                                                                                                                                                                                     
for file in *.zip; do                                                                                                                                                                                  

nuada

#!/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

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] }'