User: Ben_Ensembl

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Ben_Ensembl1.3k
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EMBL-EBI
Twitter:
@BENsembl
Last seen:
11 hours ago
Joined:
4 years, 2 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 90 results • page 1 of 9 • next >
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Answer: A: VEP order most severe to least
... Hi shwethacm, I'm afraid that I'm not able to help with any particular suggestions or custom scripts that will help to filter or rearrange your VCF output. However, I wanted to correct a small error in your assumption- the VEP does not necessarily arrange the output from most to least severe for ea ...
written 18 hours ago by Ben_Ensembl1.3k
0
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Comment: C: Alternative allele in VEP output
... No problem- you can use the --show_ref_allele option if you are running the command line version of VEP: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic ...
written 2 days ago by Ben_Ensembl1.3k
2
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Answer: A: Alternative allele in VEP output
... Hi A, The 'Allele' field in the VEP output is the alternative allele that is supplied in the input and that has been used to calculate the consequences for that output row. More information about the output fields can be found in the documentation: http://www.ensembl.org/info/docs/tools/vep/vep_fo ...
written 2 days ago by Ben_Ensembl1.3k
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Answer: A: (mouse) Convert hugo symbol (i think) to Ensemble ID
... Hi Wesley, Since you are querying the mouse genes, you need to use the 'mgi_symbol' filter with your list of gene names. Best wishes Ben Ensembl Helpdesk ...
written 7 days ago by Ben_Ensembl1.3k
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Comment: C: Ensembl reduced functionality: 10th March-4th April 2020
... The physical move was completed last week and we are currently in the process of rebooting different systems and slowly bringing the services back in an organised way. We actually hope that many of the services will be available again before the 4th April but it's a work in progress. ...
written 8 days ago by Ben_Ensembl1.3k
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Comment: C: Ensembl reduced functionality: 10th-4th April 2020
... Dates of data centre migration changed to 10th March-4th April to reflect current estimates of completion of works. ...
written 8 days ago by Ben_Ensembl1.3k
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Comment: C: Retrive genomic sequences of genes of all ensembl organsims
... Hi Elisheva, My suggestion regarding the GTF or GFF files was to first parse these files to retrieve the genomic coordinates of the genes. Then, in a second step, to use the Perl API to retrieve the genomic sequences relating to the regions defined by the coordinates from step 1. However, you coul ...
written 8 days ago by Ben_Ensembl1.3k
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Answer: A: SNP to CHR:POS mapping: dealing with genome patches
... Hi Petar, What is 'correct' will depend on what you want to do with the data after your mapping process. The alternative sequences (patches and haplotypes) are representations of the same region of the genome. Many people decide to work only with the primary assembly due to the redundancy of some o ...
written 9 days ago by Ben_Ensembl1.3k
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Comment: C: Retrive gene sequences of all ensembl organsims
... Hi Elisheva, Unfortunately, there is no file for the 'genomic sequences of genes' that you need available on the Ensembl FTP site. I think a combination of using the GTF/GFF files from the Ensembl FTP site to retrieve the genomic coordinates, then using the Perl API with genomic slices defined usin ...
written 9 days ago by Ben_Ensembl1.3k
0
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Comment: C: Biomart mapping ensembl_transcript_id_version
... If you enter the unversioned stable ID into the ID History Convertor, it will provide you with the timeline of the version increases and the current version number. ...
written 21 days ago by Ben_Ensembl1.3k

Latest awards to Ben_Ensembl

Scholar 7 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Scholar 22 days ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 5 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 5 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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 8 weeks ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 8 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?
Voter 8 weeks ago, voted more than 100 times.
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?
Guru 9 months ago, received more than 100 upvotes.
Teacher 9 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 10 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 13 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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?
Scholar 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 14 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 14 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Teacher 16 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?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms
Teacher 18 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 19 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 19 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms

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