Hello,
Good news - there is a new conversion program that does just what you want to
do. It is not documented on the link I gave you, but it is in the kent source
tree, same location as the other utilities. Once compiled, type the program
name to see the usage:
gff3ToGenePred - convert a GFF3 file to a genePred file
usage:
gff3ToGenePred inGff3 outGp
options:
-honorStartStopCodons - only set CDS start/stop status to complete if there
are
corresponding start_stop codon records
This converts:
- top-level gene records with mRNA records
- top-level mRNA records
- mRNA records can contain exon and CDS, or only CDS, or only
exon for non--coding.
Very glad that we could help,
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
----- "Jennifer Jackson" <[email protected]> wrote:
> From: "Jennifer Jackson" <[email protected]>
> To: "John Malone" <[email protected]>
> Cc: [email protected]
> Sent: Friday, November 6, 2009 9:31:25 PM GMT -08:00 US/Canada Pacific
> Subject: Re: [Genome] convert GFF3 to refFlat.txt (genePred)
>
> Hello,
>
> We do not have a utility to do that particular conversion, but we do
> have the reverse for an earlier version of the GTF format. Perhaps it
> would be a place to start when creating your own? It is is the kent
> source tree:
>
> gpToGtf
> http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities
>
> One option may be to try to load the data as a custom track, then
> output the data in genePred format using the Table browser. There are
> a few versions of GFF/GTF format and not all sources are consistent
> with the formatting rules. These are the description we use:
> http://genome.ucsc.edu/FAQ/FAQformat#format3
> http://genome.ucsc.edu/FAQ/FAQformat#format4
>
> Also, these prior mailing list answers may be helpful:
> Open google and paste in "gtf
> site:lists.soe.ucsc.edu/pipermail/genome"
>
> We hope this is helpful. I am not sure how familiar you are with the
> browser, but just in case, more details for the Table browser, Custom
> Tracks, etc. can be found by using the top blue navigation bar links
> Help & FAQ, but if you would like specific pointers or have a
> question, please ask.
> Jennifer
>
> ------------------------------------------------
> Jennifer Jackson
> UCSC Genome Bioinformatics Group
>
> ----- "John Malone" <[email protected]> wrote:
>
> > From: "John Malone" <[email protected]>
> > To: [email protected]
> > Sent: Friday, November 6, 2009 3:43:21 PM GMT -08:00 US/Canada
> Pacific
> > Subject: [Genome] convert GFF3 to refFlat.txt (genePred)
> >
> > Hi,
> >
> > I'd like to convert a GFF3 file into a refFlat (genePred) file. Do
>
> > you have a script that will do this?
> >
> > Thanks,
> >
> > John
> > _______________________________________________
> > Genome maillist - [email protected]
> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
