Moderator: Emily_Ensembl
Emily_Ensembl ♦ 13k
- Reputation:
- 12,950
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- Trusted
- Location:
- EMBL-EBI
- Website:
- http://www.ensembl.org...
- Twitter:
- @Ensemily
- Last seen:
- 2 hours ago
- Joined:
- 4 years, 8 months ago
- Email:
- e***********@gmail.com
Outreach Project Leader for Ensembl. I can help you with anything Ensembl-related (or find someone who can).
Posts by Emily_Ensembl
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... Usually you use a [Hardy-Weinburg equilibrium][1] to identify if a variant is under selection. In a randomly mating population where the variant is not under selection the following should be true:
p^2 + 2pq + q^2 = 1
Where p is the frequency of allele 1 and q is the frequency of allele 2.
...
written 4 hours ago by
Emily_Ensembl ♦ 13k
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... You can do this with BioMart. [Help video to get you started][1]. Filter by your list of gene names, get the cDNA (or even 5' UTR) sequence as attributes.
[1]: https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwi6z8KrmPzWAh ...
written 1 day ago by
Emily_Ensembl ♦ 13k
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... Working fine for me:
> library(biomaRt)
> listEnsembl()
biomart version
1 ensembl Ensembl Genes 90
2 ENSEMBL_MART_MOUSE Mouse strains 90
3 snp Ensembl Variation 90
4 regulation Ensembl Regulati ...
written 7 days ago by
Emily_Ensembl ♦ 13k
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Comment:
C: Cosmic Database using BioMart
... You might be best downloading the VCF then using [vcf-tools][1] to filter
[1]: https://vcftools.github.io/perl_module.html ...
written 8 days ago by
Emily_Ensembl ♦ 13k
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Answer:
A: Cosmic Database using BioMart
... You use the Ensembl variation somatic variation database to access COSMIC data:
cosmicMart = useEnsembl (biomart="snp", dataset = hsapiens_snp_som")
If you're looking to download the whole COSMIC database, BioMart is not a suitable way to do this. Please download the somatic VCF files from the ...
written 9 days ago by
Emily_Ensembl ♦ 13k
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... You could find the [precomputed alignments][1] in Ensembl Plants.
[1]: http://plants.ensembl.org/Arabidopsis_thaliana/Location/Compara_Alignments?r=1:8001-18000 ...
written 9 days ago by
Emily_Ensembl ♦ 13k
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... You could put the HGVSc notation into the [Ensembl VEP][1].
[1]: http://www.ensembl.org/info/docs/tools/vep/index.html ...
written 10 days ago by
Emily_Ensembl ♦ 13k
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... I'm assuming women need not apply? ...
written 11 days ago by
Emily_Ensembl ♦ 13k
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204
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... I'm assuming women need not apply? ...
written 11 days ago by
Emily_Ensembl ♦ 13k
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... We don't have BioMart for genomes in pre. These are genomes that have not yet been fully processed and do not have the full file structure, which means we don't have the BioMart tables. Crab eating macaque is due to appear in the next Ensembl release, due in December. ...
written 18 days ago by
Emily_Ensembl ♦ 13k
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