User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl1.5k
Reputation:
1,480
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
2 days, 6 hours ago
Joined:
4 years, 6 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 109 results • page 1 of 11 • next >
1
vote
1
answer
109
views
1
answers
Comment: C: Description of fasta file from human transcriptom Gencode
... No problem - I think you mean the FASTA file of transcript sequences from here: https://www.gencodegenes.org/human/ In that case, you can refer to my description above. More information about the header content can be found in the README on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/gencode/_R ...
written 5 weeks ago by Ben_Ensembl1.5k
3
votes
1
answer
109
views
1
answers
Answer: A: Description of fasta file from human transcriptom Gencode
... Hi v.shapovalova1, I'm not sure where you found this header or where it comes from. However, OR4F5-201 - transcript name OR4F5 - gene name 1054 - transcript length (base pairs) UTR5:1-36 - coordinates of 5' UTR relative to transcript CDS:37-95 - coordinates of CDS relative to transcript UTR3:955- ...
written 5 weeks ago by Ben_Ensembl1.5k
1
vote
0
answers
104
views
0
answers
Comment: C: Annotate hs37d5 genome calls using VEP
... Hi igor, The VEP can annotate variants using a custom cache defined in GFF/GTF files supplied in the VEP query. More information can be found on the following documentation page: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#gff Best wishes Ben Ensembl Helpdesk ...
written 6 weeks ago by Ben_Ensembl1.5k
1
vote
1
answer
111
views
1
answers
Answer: A: Downloading Ensembl regulatory build hg38
... Hi AISHA, I'm not sure which file you have downloaded but this is the FTP directory with the current Ensembl regulatory build for human: http://ftp.ensembl.org/pub/current_regulation/homo_sapiens/ Best wishes Ben ...
written 8 weeks ago by Ben_Ensembl1.5k
1
vote
1
answer
90
views
1
answers
Answer: A: NA return when searching for 3'UTRs in biomaRt
... Hi beccafhhs, Have you checked whether the transcripts of the omitted genes have annotated UTRs using Ensembl: www.ensembl.org From the large number of genes in your list, I suspect that those missing UTR sequence will be non-coding, and so will not have UTR sequences. Best wishes Ben ...
written 8 weeks ago by Ben_Ensembl1.5k
0
votes
1
answer
132
views
1
answers
Answer: A: VEP and gnomAD AF inconsistencies
... Hi cocchi.e89, By default the VEP only reports allele frequencies from the gnomAD exomes dataset. However, you can configure the VEP to retrieve allele frequencies from the gnomAD genomes dataset via VEP's custom annotation functionality: http://www.ensembl.org/info/docs/tools/vep/script/vep_exampl ...
written 10 weeks ago by Ben_Ensembl1.5k
2
votes
1
answer
129
views
1
answers
Answer: A: VEP 100 and GRCh37
... Hi cocchi.e89, The GRCh37 FASTA files can be found here: http://ftp.ensembl.org/pub/grch37/release-100/fasta/homo_sapiens/ However, to manually install the GRCh37 cache, you can use the files found in the following directory: http://ftp.ensembl.org/pub/release-100/variation/vep/ using the instruc ...
written 11 weeks ago by Ben_Ensembl1.5k
0
votes
0
answers
99
views
0
answers
Comment: C: Cannot access Ensembl website
... Hi rthomas, It seems that you experienced some intermittent issues over the weekend but I'm glad to hear that the error now seems to be resolved. Please do contact helpdesk[at]ensembl.org if you run into any more trouble. ...
written 11 weeks ago by Ben_Ensembl1.5k
0
votes
1
answer
169
views
1
answers
Comment: C: Ensembl gene ID meaning of the underscore
... Ah, sorry - I didn't notice the files from your original post. In the GENCODE GTFs mapping versions are appended to the identifiers (eg. ENSG00000228327.3_2) in the annotation mapped back to GRCh37. More information can be found in their documentation: https://www.gencodegenes.org/pages/data_format ...
written 11 weeks ago by Ben_Ensembl1.5k
4
votes
1
answer
169
views
1
answers
Answer: A: Ensembl gene ID meaning of the underscore
... Yes, Kevin and ATpoint are correct. The underscore is not part of the Ensembl stable ID specifications. Best wishes Ben Ensembl Helpdesk ...
written 11 weeks ago by Ben_Ensembl1.5k

Latest awards to Ben_Ensembl

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 5 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 11 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Centurion 11 weeks ago, created 100 posts.
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 11 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 4 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 4 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Scholar 4 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 6 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Voter 6 months ago, voted more than 100 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Guru 13 months ago, received more than 100 upvotes.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 17 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Should ENSEMBL up- and downstream variants be classified as genic or non genic?
Scholar 17 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 18 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1388 users visited in the last hour