[miso-users] Generation of GFF3 file

[Yarden Katz]

Hi,

If you can get your file in a UCSC table format ("genePred" format), you can use genePredToGtf, a UCSC utility, to convert it to GTF and then GFF.  See:

==
http://genes.mit.edu/burgelab/miso/docs/#human-mouse-gene-models-for-isoform-centric-analyses

Annotations can be converted from UCSC table formats or from GTF format into GFF3 using the following procedure:

	• Download your gene annotation (e.g. Ensembl genes, RefSeq) from UCSC Table Browser. For example, an Ensembl genes table ensGene.txt can be downloaded for the mm9 genome from UCSC goldenPath here (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ensGene.txt.gz).
	• To convert this gene table into GFF3, use of these two ways: (a) use the script ucsc_table2gff3.pl (from biotoolbox) to convert the table directly into GFF3, or (b) use the UCSC utility genePredToGtf to convert the table into GTF format (instructions for this are described in http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format) and then convert the GTF file into GFF3 using gtf2gff3.pl.
==

There's no obvious mapping from BED to GTF/GFF, since a BED file is just a list of coordinates and does not necessarily specify gene -> mRNA -> exon structures.  You just need to output the genes, mRNAs and exon coordinates in GFF (or GTF, since's easily converted).

  --Yarden

On Feb 13, 2013, at 1:52 PM, Charizanis,Konstantinos wrote:

> Hi all,
>  
> I’m trying to generate a new polyA annotation database to use with MISO but I have the following problem.
> I have a bed file with the new annotation downloaded from GO files of Derti et. al.
> If I upload that to the UCSC genome browser and then save it as a GTF file, I cannot use the GTF2GFF3.pl script since it cannot work with GTF files generated from UCSC tables. How do I overcome that problem? How did you generate the Bin Tian’s gff3 polyA database?
> Thank you in advance,
>  
> Konstantinos
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