<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I converted GTF file (generated by Cufflinks) to GFF3 format using Cufflinks using the following command:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">gffread -E merged.gtf -o- >merged_gtfToGff3.gff3<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I try to index merged_gtfToGff3.gff3 file using MISO I see that 0 genes were loaded and genes.gff file is 0.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">[akulan@helix stringtieGtfs_v1-0-3_cuffmerged]$ index_gff --index merged_gtfToGff3.gff3 mergedIndexedGff/<o:p></o:p></p>
<p class="MsoNormal">Indexing GFF...<o:p></o:p></p>
<p class="MsoNormal"> - GFF: /akulan/merged_gtfToGff3.gff3<o:p></o:p></p>
<p class="MsoNormal"> - Outputting to: / akulan/mergedIndexedGff<o:p></o:p></p>
<p class="MsoNormal">Loaded 0 genes<o:p></o:p></p>
<p class="MsoNormal"> - Loading of genes from GFF took 199.95 seconds<o:p></o:p></p>
<p class="MsoNormal">Outputting gene records in GFF format...<o:p></o:p></p>
<p class="MsoNormal"> - Output file: /gpfs/gsfs4/users/akulan/transcriptome/stringtie/stringtieGtfs_v1-0-3_cuffmerged/mergedIndexedGff/genes.gff<o:p></o:p></p>
<p class="MsoNormal"> - Serialization of genes from GFF took 13.24 seconds<o:p></o:p></p>
<p class="MsoNormal">Indexing of GFF took 213.18 seconds.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here are the top 5 lines from the gff3 file<o:p></o:p></p>
<p class="MsoNormal"># gffread -E merged.gtf -o-<o:p></o:p></p>
<p class="MsoNormal">##gff-version 3<o:p></o:p></p>
<p class="MsoNormal">chr1 Cufflinks transcript 11869 14409 . + . ID=TCONS_00000001;geneID=XLOC_000001;gene_name=DDX11L1<o:p></o:p></p>
<p class="MsoNormal">chr1 Cufflinks exon 11869 12227 . + . Parent=TCONS_00000001<o:p></o:p></p>
<p class="MsoNormal">chr1 Cufflinks exon 12613 12721 . + . Parent=TCONS_00000001<o:p></o:p></p>
<p class="MsoNormal">chr1 Cufflinks exon 13221 14409 . + . Parent=TCONS_00000001<o:p></o:p></p>
<p class="MsoNormal">chr1 Cufflinks transcript 11869 29022 . + . ID=TCONS_00000002;geneID=XLOC_000001;gene_name=DDX11L1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any suggestions as to why the genes are not loaded from the gff file would be really helpful.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you very much.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,<o:p></o:p></p>
<p class="MsoNormal">Nirmala<o:p></o:p></p>
</div>
</body>
</html>