gff to refflat probem

[Yulin Jin]

 Hi Sir:

I have a .gff annotation file of Ictalurus punctatus (channel catfish), which was downloaded from NCBI. Now I need to convert the .gff file to a refflat (ucsc) formatted RNA annotation file in Linux. Could you please help to get the idea and for that? Thank you.

Best

Yulin

[Matthew Speir]

Hi Yulin,

Thank you for your question about creating a "refFlat" formatted file.

The refFlat format is related to the "genePred" format, described here: http://genome.ucsc.edu/FAQ/FAQformat.html#format9. The primary difference between the two formats is the refFlat format includes an extra column at the beginning, the "geneName" column. You can use our gff3ToGenePred utility to convert your GFF file into a genePred file. You can download the utility here: http://hgdownload.soe.ucsc.edu/admin/exe/. After you've converted your file to the genePred format, you'll then have to use your own scripting method to add in the extra "geneName" column to turn your genePred file into a refFlat file. You'll have to decide what you want to put in this column. In the refFlat table in our genome databases, we use the gene symbol, e.g. SOD1, DKC1, or HUNK.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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