Getting linked exons BED from UCSC tables

Today I needed bigBed file for visualization of transcript positions in a browser which is bigBed and bigWig based. I have found a discussion where Katrina Learned from UCSC Genome Bioinformatics Group posted very usefull script. I am not going to reinvent the wheel.

nano genePredToBed

and paste this

#!/usr/bin/awk -f

#
# Convert genePred file to a bed file (on stdout)
#
BEGIN {
     FS="\t";
     OFS="\t";
}
{
     name=$1
     chrom=$2
     strand=$3
     start=$4
     end=$5
     cdsStart=$6
     cdsEnd=$7
     blkCnt=$8

     delete starts
     split($9, starts, ",");
     delete ends
     split($10, ends, ",");
     blkStarts=""
     blkSizes=""
     for (i = 1; i <= blkCnt; i++) {
         blkSizes = blkSizes (ends[i]-starts[i]) ",";
         blkStarts = blkStarts (starts[i]-start) ",";
     }

     print chrom, start, end, name, 1000, strand, cdsStart, cdsEnd, 0, 
blkCnt, blkSizes, blkStarts
}

We are almost ready to make our bed file:

chmod +x genePredToBed
wget http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/knownGene.txt.gz
gzip -d knownGene.txt.gz
cat knownGene.txt | ./genePredToBed > known.bed

Now we can use Jim Kent's bedToBigBed and we are done.

Getting GTF from UCSC with proper gene_id

While downloading GTF file (knownGenes or ensemblGenes) from UCSC Table browser an output has one serious issue. Transcript_id = gene_id. And in fact there is no gene_id. Below simple solution is presented for this problem (mm9 genome):

#prerequisities mysql
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf
chmod +x genePredToGtf
sudo ln -s ./genePredToGtf genePredToGtf
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e "select * from ensGene;" mm9 | cut -f2- | genePredToGtf file stdin ensGene.gtf

Converting between .gff, .gtf and .bed formats

Various NGS analysis tools require various input formats. It is sometimes tricky to make free software working.
Recently, all required tools for converting between .gff, .gtf and .bed formats were incorporated into Tubingen Rätsch Lab Galaxy instance

http://galaxy.tuebingen.mpg.de/