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Dear Wibowo,<br>
<br>
This is a off-by-one error affecting features on the Y chromosome.<br>
This has been fixed in our dumping code and corrected files will be
available in release 90.<br>
<br>
<br>
Kind regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 06/06/2017 08:40, Wibowo Arindrarto
wrote:<br>
</div>
<blockquote
cite="mid:D6PdPICauqraqwsk5a5aEgAYknKg1WeCwX72ANuDBAcMvNiQKoiqJVbGCYM0pR1UAEnP3GglKIjOsNtjsQI3rMY7Ob2fD7mJ5OaCItMKWlw=@bow.web.id"
type="cite">
<div>Dear Ensembl developers,<br>
<br>
I was wondering what the rules are for stop codon and CDS
features in GTF files released by Ensembl. Should stop codons be
part of a CDS feature?<br>
<br>
As far as I understand, they should not be (also referring to
this Biostar post to which Ensembl replied: <a
moz-do-not-send="true"
href="https://www.biostars.org/p/206362/">https://www.biostars.org/p/206362/</a>).
However, I stumbled on a transcript in the release 89 GTF (Homo
sapiens) that has a stop codon included as part of a CDS. This
is transcript ENST00000383070 and I am pasting the relevant
columns below ($ grep ENST00000341290 {gtf} | cut -f1,3,4,5,7) :<br>
<br>
</div>
<div class="protonmail_signature_block
protonmail_signature_block-empty">
<div class="protonmail_signature_block-user
protonmail_signature_block-empty">Y ensembl_havana transcript
2786855 2787699 . -<br>
</div>
</div>
<div>Y ensembl_havana transcript 2786855 2787699 -<br>
</div>
<div>Y ensembl_havana exon 2786855 2787699 -<br>
</div>
<div>Y ensembl_havana CDS 2786989 2787603 -<br>
</div>
<div>Y ensembl_havana start_codon 2787601 2787603 -<br>
</div>
<div>Y ensembl_havana stop_codon 2786989 2786991 -<br>
</div>
<div>Y ensembl_havana five_prime_utr 2787604 2787699 -<br>
</div>
<div>Y ensembl_havana three_prime_utr 2786855 2786988 -<br>
</div>
<div class="protonmail_signature_block
protonmail_signature_block-empty">
<div class="protonmail_signature_block-user
protonmail_signature_block-empty">Y ensembl_havana
three_prime_utr 2786855 2786988 . -<br>
</div>
</div>
<div><br>
</div>
<div>As you can see, the stop codon spans position 2786989
and 2786991, but position 2786989 onwards is already part of the
(only) CDS of the transcript.<br>
<br>
Would somebody clarify whether this is intentional or not?</div>
<div><br>
</div>
<div>With kind regards,<br>
</div>
<div>Wibowo Arindrarto</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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