gff to refFlat

[David Lyon]

I am looking to convert gff files to refFlat

does anyone have any scripts I can use to do this conversion?

Thanks

[marcora]

Do you mean refFlat to GFF?

[btuser]

Do you know of any script that I can use to convert refFlat to GFF3 or raw juncs format for use with TopHat?

[marcora]

Do you know of any script that I can use to convert refFlat to GFF3 or raw juncs format for use with TopHat?

Download refFlat in GTF format from UCSC and then convert to GFF3 using the script found here:

http://seqanswers.com/forums/showthread.php?t=3201

[btuser]

Thank you!