[ensembl-dev] Sequence for ENSMUST00000198176 not in FASTA files

[mag]

Hi Charlie,

This looks like a bug to me, we will investigate this into more detail 
and get back to you.


Kind regards,
Magali

On 10/05/2017 12:29, Charles Joseph Murphy wrote:
> Thanks, Magali.
>
> However running the following command:
>
> gzip -cd Mus_musculus.GRCm38.ncrna.fa.gz | grep 
> 'transcript_biotype:TEC' | wc -l
>
> I get 33 transcripts that also have the TEC classification?
>
> Charlie
>
>
>> On May 10, 2017, at 04:33, mag <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>> 
>> wrote:
>>
>> Hi Charlie,
>>
>> The transcript ENSMUST00000198176 has a biotype TEC, which stands for 
>> To Be Experimentally Confirmed.
>> 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.
>>
>> We are currently reviewing this decision and might be able to provide 
>> the sequence in future releases.
>>
>>
>> Kind regards,
>> Magali
>>
>> On 10/05/2017 04:57, Charles Joseph Murphy wrote:
>>> Hi,
>>>
>>> I notices that for GRCm38 release 88 the sequence for the 
>>> transcript ENSMUST00000198176 is not present in any of the following 
>>> files:
>>>
>>> ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus/ncrna//Mus_musculus.GRCm38.ncrna.fa.gz 
>>> <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=>
>>> ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus/cdna//Mus_musculus.GRCm38.cdna.abinitio.fa.gz 
>>> <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=>
>>> ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus/cdna//Mus_musculus.GRCm38.cdna.all.fa.gz 
>>> <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=>
>>> ftp://ftp.ensembl.org/pub/release-88/fasta/mus_musculus//cds/Mus_musculus.GRCm38.cds.all.fa.gz 
>>> <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=>
>>>
>>> What is the reason?
>>>
>>> Thanks,
>>> Charlie
>>>
>>>
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