<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Charlie,<br>
<br>
This looks like a bug to me, we will investigate this into more
detail and get back to you.<br>
<br>
<br>
Kind regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 10/05/2017 12:29, Charles Joseph
Murphy wrote:<br>
</div>
<blockquote
cite="mid:0B715225-12F9-4B9A-A452-3592DE027D08@med.cornell.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Thanks, Magali.
<div class=""><br class="">
</div>
<div class="">However running the following command:</div>
<div class=""><br class="">
</div>
<div class="">gzip -cd Mus_musculus.GRCm38.ncrna.fa.gz | grep
'transcript_biotype:TEC' | wc -l</div>
<div class=""><br class="">
</div>
<div class="">I get 33 transcripts that also have the TEC
classification?</div>
<div class=""><br class="">
</div>
<div class="">Charlie</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On May 10, 2017, at 04:33, mag <<a
moz-do-not-send="true" href="mailto:mr6@ebi.ac.uk"
class="">mr6@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">Hi Charlie,<br
class="">
<br class="">
The transcript ENSMUST00000198176 has a biotype TEC,
which stands for To Be Experimentally Confirmed.<br
class="">
Due to its ambiguous nature, transcripts of that biotype
are not part of any of our biotype classifications,
hence not dumped out in the FASTA files.<br class="">
<br class="">
We are currently reviewing this decision and might be
able to provide the sequence in future releases.<br
class="">
<br class="">
<br class="">
Kind regards,<br class="">
Magali<br class="">
<br class="">
<div class="moz-cite-prefix">On 10/05/2017 04:57,
Charles Joseph Murphy wrote:<br class="">
</div>
<blockquote
cite="mid:B0F4D7E8-4036-4DCA-92D7-9A64321C2B5E@med.cornell.edu"
type="cite" class="">
Hi,
<div class=""><br class="">
</div>
<div class="">I notices that for GRCm38 release 88 the
sequence for the transcript ENSMUST00000198176 is
not present in any of the following files:</div>
<div class=""><br class="">
</div>
<div class=""><a moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ensembl.org_pub_release-2D88_fasta_mus-5Fmusculus_ncrna__Mus-5Fmusculus.GRCm38.ncrna.fa.gz&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=P8Crx2lb50Z2HaGvcFsC2Weh3Whyyf-E5EfjCV5nnBE&e="
class="">ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus/ncrna//Mus_musculus.GRCm38.ncrna.fa.gz</a></div>
<div class=""><a moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ensembl.org_pub_release-2D88_fasta_mus-5Fmusculus_cdna__Mus-5Fmusculus.GRCm38.cdna.abinitio.fa.gz&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=tDsckNxZwOc8DGrkbozqkxlB_0CyDw-u4F7tq59jABo&e="
class="">ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus/cdna//Mus_musculus.GRCm38.cdna.abinitio.fa.gz</a></div>
<div class=""><a moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ensembl.org_pub_release-2D88_fasta_mus-5Fmusculus_cdna__Mus-5Fmusculus.GRCm38.cdna.all.fa.gz&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=cUXvnj8Qd9pSX5NUl-rGoRNl9s2MHFv_vDaIVQXSnYU&e="
class="">ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus/cdna//Mus_musculus.GRCm38.cdna.all.fa.gz</a></div>
<div class=""><a moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.ensembl.org_pub_release-2D88_fasta_mus-5Fmusculus__cds_Mus-5Fmusculus.GRCm38.cds.all.fa.gz&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=T9BHw_4iBxATgBz_7LrLwLxwKYmtoH8XDM07ocYQPNI&e="
class="">ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus//cds/Mus_musculus.GRCm38.cds.all.fa.gz</a></div>
<div class=""><br class="">
</div>
<div class="">What is the reason?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Charlie</div>
<br class="">
<fieldset class="mimeAttachmentHeader"></fieldset>
<br class="">
<pre class="" wrap="">_______________________________________________
Dev mailing list <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ensembl.org_mailman_listinfo_dev&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=1FQ5Ufcc2TFm3N_L5h_Nr3_cDFY7gNigJoBJhq4-S9Q&e=">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=YERIwZX803tez6_Cswocqne9zKXJmFarFk6jzlyLjoE&e=">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br class="">
</div>
_______________________________________________<br
class="">
Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br
class="">
Posting guidelines and subscribe/unsubscribe info: <a
moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ensembl.org_mailman_listinfo_dev&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=1FQ5Ufcc2TFm3N_L5h_Nr3_cDFY7gNigJoBJhq4-S9Q&e="
class="">
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ensembl.org_mailman_listinfo_dev&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=1FQ5Ufcc2TFm3N_L5h_Nr3_cDFY7gNigJoBJhq4-S9Q&e=</a>
<br class="">
Ensembl Blog: <a moz-do-not-send="true"
href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=YERIwZX803tez6_Cswocqne9zKXJmFarFk6jzlyLjoE&e="
class="">
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=6_8p0CcRADDFEUqXX8FZ2k2yCjJHyoxyDfHQ_BEN7iY&s=YERIwZX803tez6_Cswocqne9zKXJmFarFk6jzlyLjoE&e=</a>
<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>