Prepare the reference genome

Download and prepare the reference genome

  • A list of available genomes is at
  • We download the full data set, but it’s possible to interrupt the download during xenoMrna (not needed, too big).
  • md5sum is a basic utility that should be present in your system, otherwise check your packages (yum, apt-get, ...)
# location of genome data that can be shared among users
mkdir -p $GENOMEDIR

rsync -avzP rsync://$GENOME/bigZips/ .

# check downloaded data integrity
md5sum -c md5sum.txt
cat *.md5 | md5sum -c

Now unpack the genome. This process differs for different genomes - some are in single .fa, some are split by chromosomes. Some archives are tarbombs, so unpack to directory chromFa to avoid a possible mess:

mkdir chromFa
tar xvzf chromFa.tar.gz -C chromFa

Create concatenated genome, use Heng Li’s sort-alt to get the common ordering of chromosomes:

find chromFa -type f | sort-alt -N | xargs cat > $GENOME.fa

Download all needed annotations

Annotation data is best obtained in UCSC table browser in BED format and then sorted and indexed by BEDtools

For example:

# directory where annotations are stored
sortBed -i $ANNOT/ensGene.bed > $ANNOT/ensGene.sorted.bed
bgzip $ANNOT/ensGene.sorted.bed
tabix -p bed $ANNOT/ensGene.sorted.bed.gz

FIXME: rozepsat Or using compressed files:

zcat -d $ANNOT/refSeqGenes.bed.gz | sortBed | bgzip > $ANNOT/refSeqGenes.sorted.bed.gz
zcat -d $ANNOT/ensGenes.bed.gz | sortBed | bgzip > $ANNOT/ensGenes.sorted.bed.gz
tabix -p bed $ANNOT/ensGenes.sorted.bed.gz
tabix -p bed $ANNOT/refSeqGenes.sorted.bed.gz

Build indexes for all programs used in the pipeline

Some programs need a preprocessed form of the genome, to speed up their operation.

# index chromosome positions in the genome file for samtools
samtools faidx $GENOMEFA

# build gmap index for zebra finch
# with some newer versions it is necessary to use -B <path/to/bindir>
# beware, this requires quite a lot of memory (gigabytes)

# smalt index
# needed only for speeding up sim4db
mkdir -p $GENOMEDIR/smalt
smalt index -s 4 $SMALT_IDX $GENOMEFA

# convert to blat format