Hi Courtney, The reason why you are getting empty output is because there are records of type "transcript" that are the parent of exons instead of "mRNA".
Hope this helps. If you have further questions, please don't hesitate to contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Courtney Babbitt" <[email protected]> To: [email protected] Sent: Friday, December 17, 2010 7:25:45 AM Subject: [Genome] gff3 to genePred Hi, I had a questions regarding a gff3 file I've been working with. I'd like to get it into genePred format using gff3ToGenePred. When I add the header "##gff-version 3" to the top of the file (pasted below), the program runs, but the program seems to produce an empty output. Any suggestions would be great! Thanks, Courtney Scaffold10075 GLEAN3 gene 592 17860 . - . ID=SPU_000001gn;Name=SPU_000001; Scaffold10075 GLEAN3 transcript 592 17860 . - . ID=SPU_000001tr;Parent=SPU_000001gn;Dbxref=SpBase:SPU_000001,Baylor_Sp:SPU_000001;Alias=GLEAN3_00001,NA; Scaffold10075 GLEAN3 exon 16289 17860 . - . ID=SPU_000001:0;Name=SPU_000001:0;Parent=SPU_000001tr; Scaffold10075 GLEAN3 exon 13980 14135 . - . ID=SPU_000001:1;Name=SPU_000001:1;Parent=SPU_000001tr; The link to the full file is also here: http://www.duke.edu/~dag23/problemFiles/GLEAN.gff3-2.5-v2-chado _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
