[miso-users] RE : Run miso with rat genome?

[Delong, Zhou]

Hi
Thanks for the reply. And thanks to Brad Friedman [brad.aaron.friedman at gmail.com] as well, who showed me this trick yesterday.
Best
Delong

________________________________________
De : Yarden Katz [yarden at MIT.EDU]
Envoyé : 19 février 2014 18:14
À : Delong, Zhou
Cc : miso-users at mit.edu
Objet : Re: [miso-users] Run miso with rat genome?

Hi,

We do not have exon-centric alternative event annotations for Rat yet, but it's on the list.  You can use whole isoform annotations, by downloading them from UCSC or Ensembl.  For example, if you download the annotations from UCSC, you can get the ensGene format in genePred format and then convert it to GFF.  Similarly, you can get GTF files and then convert them to GFF for the annotation of interest.  There are plenty of standard scripts for doing this.  One way to do this is with the ucsc_table2gff.pl script:

$ ucsc_table2gff3.pl --ftp ensgene --db rn4 --table ensGene

The script is hosted here: https://github.com/yarden/rnaseqlib/blob/clip/scripts/ucsc_table2gff3.pl


Best, --Yarden


On Feb 17, 2014, at 11:28 AM, Delong, Zhou wrote:

> Hello,
> I have some Tophat outputs from rat cells and I would like to run miso to calculat PSIs for alternatively spliced exons.
> I have rat genome RN4 from UCSC but I don't have any .gff to index.
> Has anyone run miso for rats and would kindly provide a .gff for RN4 or knows how to generate a .gff from a reference genome?
> Thanks in advance,
> Delong ZHOU
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users

--
Yarden Katz <yarden at mit.edu>