inquire about gff3ToGenePred
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qingpol
Feb 23, 2015, 11:59:25 AM2/23/15
to gen...@soe.ucsc.edu
Dear Sir/Madam,
I am trying to using gff3ToGenePred to convert my rice gff3 file to the
UCSC format. However, when running, the softwares reports that “CDS must
have phase”, and then terminated.
So my question is if there are no “CDS phase” information in the gff3
file, the gff3ToGenePred can not work normally?
I attached a test.gff3 file for you to test the software.
I am looking forward to your response.
Thank you!
Qingpo Liu
I am trying to using gff3ToGenePred to convert my rice gff3 file to the
UCSC format. However, when running, the softwares reports that “CDS must
have phase”, and then terminated.
So my question is if there are no “CDS phase” information in the gff3
file, the gff3ToGenePred can not work normally?
I attached a test.gff3 file for you to test the software.
I am looking forward to your response.
Thank you!
Qingpo Liu
Steve Heitner
Feb 23, 2015, 3:38:55 PM2/23/15
to qingpol, gen...@soe.ucsc.edu
Hello, Qingpo.
The GFF specification (http://genome.ucsc.edu/FAQ/FAQformat.html#format3) requires that any coding exon must have a value between 0-2 in the "frame" field. All of your entries have a "." in this field.
Note that there is an online tool to validate GFF3 files at http://genometools.org/cgi-bin/gff3validator.cgi. Running your test file through the validator produces an error.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
--
The GFF specification (http://genome.ucsc.edu/FAQ/FAQformat.html#format3) requires that any coding exon must have a value between 0-2 in the "frame" field. All of your entries have a "." in this field.
Note that there is an online tool to validate GFF3 files at http://genometools.org/cgi-bin/gff3validator.cgi. Running your test file through the validator produces an error.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
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