Re: [Genome] Full transcriptome GTF files; hg19, custom track and whole genome

[Katrina Learned]

Hi John,

If your GTF is ~1.5 million lines or less, please gzip it and try 
uploading it. If your GTF is significantly larger and/or the upload 
fails for some other reason, you may need to do the extra work to 
convert to bigBed. Doing so will take a few steps:

gtfToGenePred (which can be obtained from 
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/)
genePredToBed (a simple awk script pasted at the end of my message)
bedToBigBed (also obtained from 
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/)

The first two commands could be run in a pipe:

gtfToGenePred my.gtf stdout | genePredToBed > my.bed

gtfToGenePred can accept a .gtf.gz. bedToBigBed can't take a pipe as 
input because it does several passes on the input file, so it has to be 
a real bed file (and not .bed.gz either). The bed file doesn't have to 
be kept after the bigBed file is created.

Please contact the mail list (genome@soe.ucsc.edu) again if you have any 
further questions.

Katrina Learned
UCSC Genome Bioinformatics Group

#!/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
}




John Herbert wrote, On 04/15/11 07:31:
> Dear Genome browsers,
> Please can you tell me how to display a full genomes/transcriptomes worth of 
> transcripts in the hg19 genome browser?
>
> I make the assumption that a full transcriptome GTF file is too big and I was 
> thinking of writing a GTF to Bed script (then to bigbed) so I can display it.
>
> I did not find the answer in your archive and will appreciate  any advice or 
> program that does GTF to Bed.
>
> Thank you in advance,
>
> Kind regards,
>
> John.
>
> _______________________________________________
> Genome maillist  -  Genome@soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>   
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