problem with GTF for pombe

Question

[Parham]

Hi,

Can some one look into this GTF file and see if there is anything wrong with it? I continuously get error message by the program I am using it with.

The GTF file is for S. pombe (fission yeast). Unfortunately I cannot find it's GTF file from anywhere and this one I have from past when pombase had it on their webpage. It seems they removed it, I wonder why?!

Cheers,
Parham

[h.mon]

The iGenomes page has two versions of the S. pombe genome. As far as I now, all genomes available there have a GTF annotation (and BWA and Bowtie indices, and more). It is a bulky download if you want just the GTF, but if you can't find it anywhere else...

Check the files though, chrom29 was missing from the USCS bosTau8, I don't know if they fixed it. Other genomes may have problems as well.

[Parham]

Yes I saw that. But the iGenomes attribute column doesn't match with UCSC format. In UCSC they it says the attributes should start with gene_id and transcript_id but the iGenomes starts with exon_id and etc. I wonder if it's an agreed file format why there are so many different variants out there published by these organizations!

Answer 1

[mark.mcdowall]

Hi Parham,

For each release PomBase updates the GFF3 files and makes them available via the FTP site (ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Chromosome_Dumps/gff3/). The reason for moving to GFF3 is that it allowed for describing features at different genomic levels (gene, transcript, exon)

If you do need the files in GTF format you can obtain these via the Ensembl Genomes FTP site which has the same gene models (ftp://ftp.ensemblgenomes.org/pub/release-29/fungi/gtf/schizosaccharomyces_pombe/ ).

For further information about updates to S. pombe I would recommend signing up to the pombe mailing list at http://www.pombase.org/about/pombe-mailing-list

There is also an ensembl-dev mailing list that highlights when there are new releases of ensembl and ensembl genomes. Details of which can be found at http://ensemblgenomes.org/info/about/contact/mailing

Updates and announcement are also made via Twitter @PomBase and @ensemblgenomes

[Parham]

Hi Mark,

Thanks a lot for thorough explanation. I found the files that I needed but still its valuable to know where to look for files in future and how to get updates.