Creating track hubs for the UCSC genome browser with BAM files

One of the projects that I am currently involved deals with the detection of novel long non-coding RNAs regulating the WNT signaling pathway in colon cancer. Since we have had our own local installation of the UCSC genome browser for some time now (and it makes a huge difference), I decided that it would be useful to gather some current knowledge about annotated human and mouse lincRNAs from a few sources. These sources are:
Human
- The Ensembl┬áGRCh37 genome annotation
- The NONCODE project
- The Broad institute lincRNA catalogue
Mouse
- The Ensembl┬áGRCm38 genome annotation
- The NONCODE project
The NONCODE project contains lincRNAs mapped to the hg19 and mm10 genomes while the Broad institute lincRNA catalogue, lincRNAs mapped to hg19. As our current browser installation has also mm9 and hg18, we will have to use the liftOver tool (in command line) and the transformation chain files to adjust the coordinates.
One way to create these tracks is to convert them to BED or bigBed formats. The best format for this representation is definitely BED. But because I have customized my pipelines in order to work mostly with bigBed and bigWig data, I thought of using bigBed instead. However, it is possible that the bedToBigBed tool from the kent utilities┬ádoes not seem to work well with small BEDn (n=6 or 12) files as I had a lot of problems with it using a lot of option combinations. So I decided to use BAM format instead and put them in a track hub. The following shell script automates the whole procedure and you can adjust it to any custom tracks you might need. In order to execute it, you will need the following:
The Kent utilities from UCSC
The BED tools
The SAM tools
The gtf2bed perl conversion script from ea-utils
The shell script creates the necessary directories, downloads the lincRNA annotations, lifts them over, converts them to BAM format, places them to the proper locations and writes the necessary files to configure the track hub.
#!/bin/bash

# We must be under sudo
if [ `id -u` -ne 0 ]; 
then
        echo "You must execute this script as root!"
        exit 1
fi

# Paths
BIGDATA_DATA_HTTP=http://your_local_bigwig_or_bigdata_server
BIGDATA_DATA_PATH=/your/loca/bigwig/or/bigdata/path
UCSC_BIN=/path/to/ucsc/kent/tools
BEDTOOLS_BIN=/path/to/bedtools
SAMTOOLS_BIN=/path/to/samtools
GTF2BED="perl /path/to/gtftobed/gtf2bed.pl"
LIFTOVER=/path/to/ucsc/kent/tools/liftOver

# Check about the dirs
if [ -d $BIGDATA_DATA_PATH ]
then
	echo "$BIGDATA_DATA_PATH has already been created..."
else
	mkdir -p $BIGDATA_DATA_PATH
fi

# Chrom sizes
for ORG in hg18 hg19 mm9 mm10
do
	if [ -f $ORG."chrom.size" ]	
	then
		echo "$ORG.chrom.size has already been created..."
	else
		$UCSC_BIN/fetchChromSizes $ORG > $ORG".chrom.size"
	fi
done

echo "==================== FETCHING DATA..."

# Ensembl, keep in mind that there is no linc characterization in hg18 or mm9 so we must liftOver...
# hg19
wget ftp://ftp.ensembl.org/pub/release-70/gtf/homo_sapiens/Homo_sapiens.GRCh37.70.gtf.gz
# mm10
wget ftp://ftp.ensembl.org/pub/release-70/gtf/mus_musculus/Mus_musculus.GRCm38.70.gtf.gz

# Broad institute lincRNA catalog, hg19 only
wget http://www.broadinstitute.org/genome_bio/human_lincrnas/sites/default/files/lincRNA_catalog/lincRNAs_transcripts.bed
wget http://www.broadinstitute.org/genome_bio/human_lincrnas/sites/default/files/lincRNA_catalog/lincRNAs_transcripts_stringentSet.bed

# NONCODE database
# hg19
wget http://www.noncode.org/NONCODERv3/datadownload/lncRNA_human.zip
# mm10
wget http://www.noncode.org/NONCODERv3/datadownload/lncRNA_mouse.zip

echo "==================== UNCOMPRESSING DATA..."

zcat Homo_sapiens.GRCh37.70.gtf.gz | grep -P '^\d+|MT' | awk '{ if ($2 ~ /lincRNA/) print "chr"$0 }' | sed s/^chrMT/chrM/g > ensembl.hg19.lincRNAs.GRCh37.70.gtf
zcat Mus_musculus.GRCm38.70.gtf.gz | grep -P '^\d+|MT' | awk '{ if ($2 ~ /lincRNA/) print "chr"$0 }' | sed s/^chrMT/chrM/g > ensembl.mm10.lincRNAs.GRCm38.70.gtf
unzip lncRNA_human.zip
mv ./human/human.bed ./
rm -r ./human
unzip lncRNA_mouse.zip
mv ./mouse/mouse.bed ./
rm -r mouse
grep -vP 'rand|chrUn|hap' lincRNAs_transcripts.bed | sort -k1,1 -k2g,2 | sed s/'0\.0'/0/g > lincRNAs_transcripts.flt.bed
sort -k1,1 -k2g,2 human.bed | awk '{ print $1"\t"$2"\t"$3"\t"substr($4,2)"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12 }' > human.srt.hg19.bed
sort -k1,1 -k2g,2 mouse.bed | awk '{ if ($5>1000) print $1"\t"$2"\t"$3"\t"substr($4,2)"\t"1000"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12; else print $0; }' | grep -v '*' > mouse.srt.mm9.bed

echo "==================== CONVERTING DATA..."

# Convert the Ensembl gtf files to bed to make bigBeds later
$GTF2BED ensembl.hg19.lincRNAs.GRCh37.70.gtf | sort -k1,1 -k2g,2 > ensembl.hg19.lincRNAs.GRCh37.70.bed
$GTF2BED ensembl.mm10.lincRNAs.GRCm38.70.gtf | sort -k1,1 -k2g,2 > ensembl.mm10.lincRNAs.GRCm38.70.bed
$LIFTOVER ensembl.hg19.lincRNAs.GRCh37.70.bed /path/to/genome/chain_files/hg19ToHg18.over.chain.gz ensembl.hg18.lincRNAs.liftOver.nsr.bed unmapped.hg18
$LIFTOVER ensembl.mm10.lincRNAs.GRCm38.70.bed /path/to/genome/chain_files/mm10ToMm9.over.chain.gz ensembl.mm9.lincRNAs.liftOver.nsr.bed unmapped.mm9
$LIFTOVER lincRNAs_transcripts.flt.bed /path/to/genome/chain_files/hg19ToHg18.over.chain.gz lincRNAs_transcripts.flt.hg18.nsr.bed unmapped.hg18
$LIFTOVER lincRNAs_transcripts_stringentSet.bed /path/to/genome/chain_files/hg19ToHg18.over.chain.gz lincRNAs_transcripts_stringentSet.hg18.nsr.bed unmapped.hg18
$LIFTOVER human.srt.hg19.bed /path/to/genome/chain_files/hg19ToHg18.over.chain.gz human.srt.hg18.bed unmapped.hg18
$LIFTOVER mouse.srt.mm9.bed /path/to/genome/chain_files/mm9ToMm10.over.chain.gz mouse.srt.mm10.bed unmapped.mm10
sort -k1,1 -k2g,2 ensembl.hg18.lincRNAs.liftOver.nsr.bed > ensembl.hg18.lincRNAs.liftOver.bed
sort -k1,1 -k2g,2 ensembl.mm9.lincRNAs.liftOver.nsr.bed > ensembl.mm9.lincRNAs.liftOver.bed
sort -k1,1 -k2g,2 lincRNAs_transcripts.flt.hg18.nsr.bed > lincRNAs_transcripts.flt.hg18.bed
sort -k1,1 -k2g,2 lincRNAs_transcripts_stringentSet.hg18.nsr.bed > lincRNAs_transcripts_stringentSet.hg18.bed

# Prepare the hub directories
for ORG in hg18 hg19 mm9 mm10
do
	if [ -d $BIGDATA_DATA_PATH/$ORG ]
	then
		echo "$BIGDATA_DATA_PATH/$ORG has already been created..."
	else
		mkdir -p $BIGDATA_DATA_PATH/$ORG
	fi
done

echo "==================== WRITING HUB..."

# Create the bigBeds to the hub directory
echo "   ================= MAKING ANNOTATION TRACKS..."
echo "      ============== Ensembl hg19..."
$BEDTOOLS_BIN/bedToBam -bed12 -i ensembl.hg19.lincRNAs.GRCh37.70.bed -g /opt/NGSTools/BEDTools/genomes/human.hg19.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.bam
echo "      ============== Ensembl hg18..."
$BEDTOOLS_BIN/bedToBam -bed12 -i ensembl.hg18.lincRNAs.liftOver.bed -g /opt/NGSTools/BEDTools/genomes/human.hg18.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.bam
echo "      ============== Ensembl mm10..."
$BEDTOOLS_BIN/bedToBam -bed12 -i ensembl.mm10.lincRNAs.GRCm38.70.bed -g /opt/NGSTools/BEDTools/genomes/mouse.mm10.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.bam
echo "      ============== Ensembl mm9..."
$BEDTOOLS_BIN/bedToBam -bed12 -i ensembl.mm9.lincRNAs.liftOver.bed -g /opt/NGSTools/BEDTools/genomes/mouse.mm9.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.bam
echo "      ============== Broad hg19..."
$BEDTOOLS_BIN/bedToBam -bed12 -i lincRNAs_transcripts.flt.bed -g /opt/NGSTools/BEDTools/genomes/human.hg19.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.bam
echo "      ============== Broad hg19 strict..."
$BEDTOOLS_BIN/bedToBam -bed12 -i lincRNAs_transcripts_stringentSet.bed -g /opt/NGSTools/BEDTools/genomes/human.hg19.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.bam
echo "      ============== Broad hg18..."
$BEDTOOLS_BIN/bedToBam -bed12 -i lincRNAs_transcripts.flt.hg18.bed -g /opt/NGSTools/BEDTools/genomes/human.hg18.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.bam
echo "      ============== Broad hg18 strict..."
$BEDTOOLS_BIN/bedToBam -bed12 -i lincRNAs_transcripts_stringentSet.hg18.bed -g /opt/NGSTools/BEDTools/genomes/human.hg18.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.bam
echo "      ============== NONCODE hg19..."
$BEDTOOLS_BIN/bedToBam -bed12 -i human.srt.hg19.bed -g /opt/NGSTools/BEDTools/genomes/human.hg19.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.bam
echo "      ============== NONCODE hg18..."
$BEDTOOLS_BIN/bedToBam -bed12 -i human.srt.hg18.bed -g /opt/NGSTools/BEDTools/genomes/human.hg18.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.bam
echo "      ============== NONCODE mm10..."
$BEDTOOLS_BIN/bedToBam -bed12 -i mouse.srt.mm10.bed -g /opt/NGSTools/BEDTools/genomes/mouse.mm10.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.bam
echo "      ============== NONCODE mm9..."
$BEDTOOLS_BIN/bedToBam -bed12 -i mouse.srt.mm9.bed -g /opt/NGSTools/BEDTools/genomes/mouse.mm9.genome | $SAMTOOLS_BIN/samtools sort - $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9
$SAMTOOLS_BIN/samtools index $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.bam

# Write the hub.txt file
echo "   ================= WRITING hub.txt..."
printf "%s\n" "hub fleming_lincRNA" > $BIGDATA_DATA_PATH/hub.txt
printf "%s\n" "shortLabel lincRNAs @Fleming" >> $BIGDATA_DATA_PATH/hub.txt
printf "%s\n" "longLabel lincRNA annotation tracks from Ensembl, Broad Institute human lincRNA catalogue and NONCODE project" >> $BIGDATA_DATA_PATH/hub.txt
printf "%s\n" "genomesFile genomes.txt" >> $BIGDATA_DATA_PATH/hub.txt
printf "%s\n" "email moulos@fleming.gr" >> $BIGDATA_DATA_PATH/hub.txt

# Write the genomes.txt file
echo "   ================= WRITING genomes.txt..."
printf "%s\n" "genome hg18" > $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n\n" "trackDb hg18/trackDb.txt" >> $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n" "genome hg19" >> $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n\n" "trackDb hg19/trackDb.txt" >> $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n" "genome mm9" >> $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n\n" "trackDb mm9/trackDb.txt" >> $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n" "genome mm10" >> $BIGDATA_DATA_PATH/genomes.txt
printf "%s\n" "trackDb mm10/trackDb.txt" >> $BIGDATA_DATA_PATH/genomes.txt

# Write the trackDb.txt files
echo "   ================= WRITING trackDb.txt files..."

# hg18
printf "%s\n" "track ensemblHg18LincRNAsLiftOver" > $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/ensembl.hg18.lincRNAs.liftOver.bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "longLabel Ensembl NCBI36 (hg18) lincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "url http://www.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "track broadHg18LincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/broad.hg18.lincRNAs.bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "shortLabel Broad lincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "longLabel Broad Institute hg18 lincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "track broadHg18LincRNAsStrict" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/broad.hg18.lincRNAs.stringent.bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "shortLabel Broad lincRNAs strict" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "longLabel Broad Institute hg18 lincRNAs strict thresholds" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "track noncodeLincRNAsHg18" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/noncode.lincRNAs.hg18.bam" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "longLabel NONCODE project hg18 lincRNAs" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt

# hg19
printf "%s\n" "track ensemblHg19LincRNAsGRCh3770" > $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/ensembl.hg19.lincRNAs.GRCh37.70.bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "longLabel Ensembl GRCh37 (hg19) lincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "url http://www.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "track broadHg19LincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/broad.hg19.lincRNAs.bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "shortLabel Broad lincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "longLabel Broad Institute hg19 lincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "track broadHg19LincRNAsStrict" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/broad.hg19.lincRNAs.stringent.bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "shortLabel Broad lincRNAs strict" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "longLabel Broad Institute hg19 lincRNAs strict thresholds" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "track noncodeLincRNAsHg19" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/noncode.lincRNAs.hg19.bam" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "longLabel NONCODE project hg19 lincRNAs" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/trackDb.txt

# mm9
printf "%s\n" "track ensemblMm9LincRNAsLiftOver" > $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm9/ensembl.mm9.lincRNAs.liftOver.bam" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "longLabel Ensembl NCBIM37 (mm9) lincRNAs" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "url http://www.ensembl.org/Mus_musculus/Search/Results?species=Mus_musculus;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "track noncodeLincRNAsMm9" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm9/noncode.lincRNAs.mm9.bam" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "longLabel NONCODE project mm9 lincRNAs" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm9/trackDb.txt

# mm10
printf "%s\n" "track ensemblMm10LincRNAsGRCm3870" > $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm10/ensembl.mm10.lincRNAs.GRCm38.70.bam" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "longLabel Ensembl GRCm38 (mm10) lincRNAs" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "url http://www.ensembl.org/Mus_musculus/Search/Results?species=Mus_musculus;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "\n" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "track noncodeLincRNAsMm10" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm10/noncode.lincRNAs.mm10.bam" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "longLabel NONCODE project mm10 lincRNAs" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm10/trackDb.txt

# Write the trackDb.txt files
echo "   ================= WRITING settings.txt files..."

# hg18
printf "%s\n" "track ensemblHg18LincRNAsLiftOver" > $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/ensembl.hg18.lincRNAs.liftOver.bam" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "longLabel Ensembl NCBI36 (hg18) lincRNAs" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "url http://www.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=\$\$" $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/ensembl.hg18.lincRNAs.liftOver.txt

printf "%s\n" "track broadHg18LincRNAs" > $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/broad.hg18.lincRNAs.bam" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "shortLabel Broad lincRNAs" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "longLabel Broad Institute hg18 lincRNAs" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.txt

printf "\n" > $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "track broadHg18LincRNAsStrict" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/broad.hg18.lincRNAs.stringent.bam" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "shortLabel Broad lincRNAs strict" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "longLabel Broad Institute hg18 lincRNAs strict thresholds" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/broad.hg18.lincRNAs.stringent.txt

printf "\n" > $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "track noncodeLincRNAsHg18" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg18/noncode.lincRNAs.hg18.bam" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "longLabel NONCODE project hg18 lincRNAs" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/hg18/trackDb.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg18/noncode.lincRNAs.hg18.txt

# hg19
printf "%s\n" "track ensemblHg19LincRNAsGRCh3770" > $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/ensembl.hg19.lincRNAs.GRCh37.70.bam" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "longLabel Ensembl GRCh37 (hg19) lincRNAs" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "url http://www.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/ensembl.hg19.lincRNAs.GRCh37.70.txt

printf "\n" > $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "track broadHg19LincRNAs" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/broad.hg19.lincRNAs.bam" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "shortLabel Broad lincRNAs" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "longLabel Broad Institute hg19 lincRNAs" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.txt

printf "\n" > $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "track broadHg19LincRNAsStrict" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/broad.hg19.lincRNAs.stringent.bam" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "shortLabel Broad lincRNAs strict" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "longLabel Broad Institute hg19 lincRNAs strict thresholds" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "color 0,192,0" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/broad.hg19.lincRNAs.stringent.txt

printf "\n" > $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "track noncodeLincRNAsHg19" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/hg19/noncode.lincRNAs.hg19.bam" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "longLabel NONCODE project hg19 lincRNAs" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/hg19/noncode.lincRNAs.hg19.txt

# mm9
printf "%s\n" "track ensemblMm9LincRNAsLiftOver" > $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm9/ensembl.mm9.lincRNAs.liftOver.bam" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "longLabel Ensembl NCBIM37 (mm9) lincRNAs" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "url http://www.ensembl.org/Mus_musculus/Search/Results?species=Mus_musculus;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm9/ensembl.mm9.lincRNAs.liftOver.txt

printf "\n" > $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "track noncodeLincRNAsMm9" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm9/noncode.lincRNAs.mm9.bam" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "longLabel NONCODE project mm9 lincRNAs" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm9/noncode.lincRNAs.mm9.txt

# mm10
printf "%s\n" "track ensemblMm10LincRNAsGRCm3870" > $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm10/ensembl.mm10.lincRNAs.GRCm38.70.bam" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "shortLabel Ensembl lincRNAs" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "longLabel Ensembl GRCm38 (mm10) lincRNAs" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "color 0,0,192" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "url http://www.ensembl.org/Mus_musculus/Search/Results?species=Mus_musculus;idx=;q=\$\$" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm10/ensembl.mm10.lincRNAs.GRCm38.70.txt

printf "\n" > $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "track noncodeLincRNAsMm10" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "type bam" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "bigDataUrl $BIGDATA_DATA_HTTP/mm10/noncode.lincRNAs.mm10.bam" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "longLabel NONCODE project mm10 lincRNAs" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "shortLabel NONCODE lincRNAs" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "boxedCfg on"  >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "color 192,0,0" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "url http://www.noncode.org/NONCODERv3/ncrna.php?ncid=\$\$" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "bamColorMode strand" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt
printf "%s\n" "showNames on" >> $BIGDATA_DATA_PATH/mm10/noncode.lincRNAs.mm10.txt

echo "==================== CLEANING UP..."
rm *.gtf* *.bed *.zip *.chrom.size *.nsr.* unmaped* *.flt.* *.srt.*

echo "==================== VERIFYING..."
chmod -R 777 /tmp/udcCache
$UCSC_BIN/hubCheck http://your_local_bigwig_or_bigdata_server/hub.txt
if [ $? != 0 ]
then
	echo "Something bad happened during hub build... Cleaning... Please check and rebuild..."
	rm -r $BIGDATA_DATA_PATH
	rm -r /tmp/udcCache/http/your_local_ip/
else
	chmod -R 777 /tmp/udcCache
	chown -R www-data:www-data /tmp/udcCache
	echo "==================== OK!"
fi
Read the script before you execute it. You will have to adjust the paths at the beginning and make other changes but I think it constitutes a good starting point. After running the script, go to the Session -> Track hubs menu of the genome browser and add http://your_local_bigwig_or_bigdata_server/hub.txt. The new tracks should appear.
Now, although the track hubs are a nice solution, they are not very good for long term customized needs, as they have to be added to user sessions and they are not enabled by default. In order to have such a cutomization, you have to hack in the UCSC genome browser database. I will show you how to do this in the next post. Keep posted!