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

Wed May 10 12:29:34 BST 2017

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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