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Hi Jose,<br>
<br>
Thank you for reporting this.<br>
<br>
We do not dump out stop or start codons that are incomplete.<br>
Unfortunately, as your example has just highlighted, having either
incomplete results in both not being dumped.<br>
<br>
Apologies for the inconvenience, this will be fixed for release 80
at the latest.<br>
Thanks again for raising this issue.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 24/03/2015 15:25, José Manuel
Rodríguez wrote:<br>
</div>
<blockquote
cite="mid:20150324152553.CA60713393A_5118201B@hx-mx2.ebi.ac.uk"
type="cite">
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<div>Hi everyone,</div>
<div><br>
</div>
<div>I have seen something strange in the GTF for human:</div>
<div>Homo_sapiens.GRCh38.79.gtf</div>
<div><br>
</div>
<div>The transcripts where the start codon (or stop codon) has
not been found</div>
<div>(labeled as “cds_start_NF” or “cds_end_NF”),</div>
<div>I don't see the coordinates of the codons which they have
found.</div>
</div>
<div><br>
</div>
<div>One example gene, “ENSG00000176571”, and the transcripts:</div>
<div>ENST00000521593 and ENST00000523299 are tagged with tag
“cds_start_NF"</div>
<div>but I don’t see the coordinates of stop_codon. Something like
this:</div>
<div>chr8<span class="Apple-tab-span" style="white-space:pre"> </span>HAVANA<span
class="Apple-tab-span" style="white-space:pre"> </span><b>stop_codon</b><span
class="Apple-tab-span" style="white-space:pre"> </span>87612061<span
class="Apple-tab-span" style="white-space:pre"> </span>87612063<span
class="Apple-tab-span" style="white-space:pre"> </span>.<span
class="Apple-tab-span" style="white-space:pre"> </span>+<span
class="Apple-tab-span" style="white-space:pre"> </span>0<span
class="Apple-tab-span" style="white-space:pre"> </span>gene_id
"ENSG00000176571.10"; transcript_id "ENST00000521593.4";
gene_type "protein_coding"; gene_status "KNOWN"; gene_name
"CNBD1"; transcript_type "protein_coding"; transcript_status
"PUTATIVE"; transcript_name "CNBD1-005"; exon_number 7; exon_id
"ENSE00002136680.1"; level 2; protein_id "ENSP00000427742.1";
tag "mRNA_start_NF"; tag "cds_start_NF";
transcript_support_level "3"; havana_gene
"OTTHUMG00000163743.5"; havana_transcript
"OTTHUMT00000375187.4";</div>
<div>chr8<span class="Apple-tab-span" style="white-space:pre"> </span>HAVANA<span
class="Apple-tab-span" style="white-space:pre"> </span><b>stop_codon</b><span
class="Apple-tab-span" style="white-space:pre"> </span>87487702<span
class="Apple-tab-span" style="white-space:pre"> </span>87487704<span
class="Apple-tab-span" style="white-space:pre"> </span>.<span
class="Apple-tab-span" style="white-space:pre"> </span>+<span
class="Apple-tab-span" style="white-space:pre"> </span>0<span
class="Apple-tab-span" style="white-space:pre"> </span>gene_id
"ENSG00000176571.10"; transcript_id "ENST00000523299.4";
gene_type "protein_coding"; gene_status "KNOWN"; gene_name
"CNBD1"; transcript_type "protein_coding"; transcript_status
"PUTATIVE"; transcript_name "CNBD1-004"; exon_number 6; exon_id
"ENSE00002099049.1"; level 2; protein_id "ENSP00000430986.1";
tag "mRNA_start_NF"; tag "cds_start_NF";
transcript_support_level "3"; tag "appris_alternative_2";
havana_gene "OTTHUMG00000163743.5"; havana_transcript
"OTTHUMT00000375186.1";</div>
<div><br>
</div>
<div><br>
</div>
<div>Is this performance correct?</div>
<div><br>
</div>
<div>Thanks in advance.</div>
<div>J</div>
<div><br>
</div>
<br>
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