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<TITLE>Re: [maker-devel] gff pass through</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>I’ve attached an example mRNAseq gff3 file from tophat/bowtie data. Could you send me your GFF3 file to debug.<BR>
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Carson<BR>
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On 2/3/10 9:47 AM, "Reith, Michael" <<a href="Michael.Reith@nrc-cnrc.gc.ca">Michael.Reith@nrc-cnrc.gc.ca</a>> wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT SIZE="2"><FONT FACE="Arial"><SPAN STYLE='font-size:10pt'>Hi all,<BR>
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I’m trying to use the gff pass through method to add the transcript/exon data generated by Cufflinks as EST information. Maker works fine if I use a fasta file for the EST input, but dies (with “Bus error”) if I try to use a gff3 file that I’ve built from the Cufflinks gtf output and validated with the on-line gff3 validator. I was wondering: 1). if the gff pass through files referred to in the Maker tutorial (pass.tar.gz) might be available to test our set up (running on Solaris); 2). whether anyone has any bright ideas on why maker would be crashing only with the gff input.<BR>
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Thanks,<BR>
Mike<BR>
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</SPAN></FONT><SPAN STYLE='font-size:10pt'><FONT FACE="Verdana, Helvetica, Arial">-----------------------------------------------------<BR>
Michael Reith<BR>
Principal Research Officer<BR>
Functional Genomics Group Leader<BR>
NRC Institute for Marine Biosciences<BR>
</FONT><FONT FACE="Arial">1411 Oxford St.<BR>
Halifax, N.S. B3H 3Z1<BR>
Canada<BR>
<BR>
phone: (902) 426-8276<BR>
fax: (902) 426-9413<BR>
email: <a href="michael.reith@nrc.ca">michael.reith@nrc.ca</a><BR>
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