annotation files

[jeffinrockey]

Dear David,

Could you please let me know what are the acceptable annotation formats usable with -a option.
I gave a gff and later a gtf. Both of them were not recognized.?

Regards,
Jeffin

[hhg7]

hi Jeffin,

thanks for letting me know.

where have you downloaded the GTF? The GTF I downloaded from refFlat on http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/ and also gencode formats.

Please send me the GTF (or link where I can download) and I can debug.

-Dave