User: Ben_Ensembl

gravatar for Ben_Ensembl
Ben_Ensembl1.6k
Reputation:
1,650
Status:
Trusted
Location:
EMBL-EBI
Twitter:
@BENsembl
Last seen:
6 hours ago
Joined:
4 years, 9 months ago
Email:
b*****@ebi.ac.uk

Posts by Ben_Ensembl

<prev • 126 results • page 1 of 13 • next >
2
votes
1
answer
44
views
1
answers
Answer: C: Retrieve 5'UTR sequences for ensembl_transcript_id's with unique start/end posit
... Hi omit3333, This will be caused by the UTR regions spanning several exons. E.g: https://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000000938;r=1:27612064-27635185;t=ENST00000374005 You'll want to take the most upstream and most downstream coordinates to get the overall start/en ...
written 6 hours ago by Ben_Ensembl1.6k
0
votes
1
answer
94
views
1
answers
Comment: C: filter_vep not filtering according to my --filter criteria
... Hi Jan, Yes, when multiple filters are used they behave like 'AND' operators. Looking in more detail, it seems that the problem is the last filter is missing some parentheses: --filter "((IMPACT is HIGH and (Aloft_pred match Recessive or Aloft_pred match Dominant)) or (REVEL > 0.5) or (VEST ...
written 12 days ago by Ben_Ensembl1.6k
1
vote
1
answer
94
views
1
answers
Answer: A: filter_vep not filtering according to my --filter criteria
... Hi Jan, The filters look alright but the input is a gzipped file, probably what is missing is the option --gz to read the file. Best wishes Ben ...
written 14 days ago by Ben_Ensembl1.6k
3
votes
0
answers
121
views
0
answers
News: Ensembl Pre! site retirement - 31st January 2021
... The [Ensembl Pre! site][1] was launched in 2003 to provide early access to preliminary data generated during the gene annotation process. Genome sequences and preliminary data were made available in the Pre! site, prior to full annotation and integration into Ensembl. Pre! data allowed researchers ...
ensembl news written 8 weeks ago by Ben_Ensembl1.6k
0
votes
0
answers
179
views
0
answers
Comment: C: bioMart ENSEMBL_MART_VEGA exists?
... You could consider using Ensembl Biomart from the Ensembl 88 archive for GRCh38 mappings (chose 'Vega' from the 'Choose Database dropdown menu'): http://mar2017.archive.ensembl.org/index.html and the Ensembl 75 archive for GRCh37 mappings: http://feb2014.archive.ensembl.org/index.html If you would ...
written 10 weeks ago by Ben_Ensembl1.6k
2
votes
1
answer
155
views
1
answers
Answer: A: Use VEP (ensembl) with specific database e.g. dbSNP 144
... Hi romain.lannes, You can install archive versions of the VEP tool that correspond to database versions that you are interested in: http://dec2015.archive.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html For example, you can see from the documentation that Ensembl 83 was the last Ensembl v ...
written 11 weeks ago by Ben_Ensembl1.6k
0
votes
1
answer
188
views
1
answers
Comment: C: About samples of RNA-seq in Ensembl database for primate and etc
... Hi, The .bam files available through the Ensembl FTP site are not always equivalent to fastq files. You can convert them, but you can’t find them in ENA as one file or id. This is due to a couple of reasons: - One of them is if there are way too many reads in one sample, we don’t keep all the rea ...
written 11 weeks ago by Ben_Ensembl1.6k
1
vote
1
answer
188
views
1
answers
Answer: A: About samples of RNA-seq in Ensembl database for primate and etc
... Hi Yu K, I've pasted my answer from the Ensembl Helpdesk for others to see: The RNA-seq data that is used in the Ensembl gene annotation process, and is available through the links you pointed towards on the Ensembl FTP site were downloaded from the European Nucleotide Archive (ENA): https://www.e ...
written 11 weeks ago by Ben_Ensembl1.6k
1
vote
2
answers
265
views
2
answers
Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... I'm glad you were able to get the VEP to run using the custom GTF and FASTA file. However, the --regulatory flag is only applicable to species with regulatory feature annotation and --gene_phenotype relies on underlying gene-phenotype associations. However, I am unable to see your output file to co ...
written 3 months ago by Ben_Ensembl1.6k
0
votes
2
answers
265
views
2
answers
Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... It seems that the VEP can't locate your cache. However, based on your query, I do not think you require the --cache option anyway. You should remove --cache from your query. ...
written 3 months ago by Ben_Ensembl1.6k

Latest awards to Ben_Ensembl

Scholar 10 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?
Scholar 3 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?
Centurion 6 months ago, created 100 posts.
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?
Scholar 6 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 8 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Scholar 8 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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?
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRt GRCh37 down?
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?
Voter 9 months ago, voted more than 100 times.
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?
Guru 17 months ago, received more than 100 upvotes.
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?
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Species not in Ensembl
Appreciated 21 months ago, created a post with more than 5 votes. For A: Inconsistencies in Using biomaRt to Retrieve HGNC Names from GO Terms

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1710 users visited in the last hour