User: Erin_Ensembl
Erin_Ensembl • 280
- Reputation:
- 280
- Status:
- Trusted
- Location:
- EMBL-EBI
- Website:
- http://www.ensembl.info/
- Twitter:
- @mycoacia
- Last seen:
- 2 days, 22 hours ago
- Joined:
- 1 year, 6 months ago
- Email:
- e*******@ebi.ac.uk
Posts by Erin_Ensembl
<prev
• 24 results •
page 1 of 3 •
next >
1
vote
1
answer
72
views
1
answers
... This is not perhaps what you are looking for in terms of guidance for analysis, but it help you identify what to look for? Ensembl has per chromosome summary statistics, number of coding or non coding genes and short variants (defined as <50bp in length), e.g. for [chromosome 1][1].
I guess what ...
written 2 days ago by
Erin_Ensembl • 280
0
votes
3
answers
86
views
3
answers
Answer:
A: Gene prediction tool
... If you're not a fan of using the command line, you could try [GenSAS][1]. I saw their presentation at PAG and from what I gather you can carry out gene annotation through their website by just supplying the raw sequencing files. They integrate popular [tools][2], so you can run everything through th ...
written 2 days ago by
Erin_Ensembl • 280
2
votes
1
answer
63
views
1
answers
Answer:
C: dbsnp for capra hircus
... ATpoint is quite right, dbSNP (relatively) recently changed to host only human data. Goat variation/phenotype data is now hosted at the European variant archive ([EVA][1]) and also [OMIA][2].
If you want to annotate your variants you can use the [variant effect predictor][3] with your VCF file, En ...
written 3 days ago by
Erin_Ensembl • 280
0
votes
2
answers
57
views
2
answers
Answer:
A: Annovar annotation for plants
... Not sure about annovar, but you can use Ensembl's variant effect predictor (VEP) [offline tool][1] with any species as long as you have the fasta file and the GTF gene annotation file, which appear to be available on the link you posted.
[1]: http://www.ensembl.org/info/docs/tools/vep/script/ve ...
written 3 days ago by
Erin_Ensembl • 280
2
votes
1
answer
50
views
1
answers
... [Tarbase][1] is a database of predicted mRNA target positions. You can find your gene in Ensembl and add the Tarbase track (click on Configure this page > Regulation > Other Regulatory regions > Tarbase > close window) in the location page, zoom into the 3' UTR and see where they are pr ...
written 4 days ago by
Erin_Ensembl • 280
3
votes
2
answers
250
views
2
answers
Answer:
A: How to use dbSNP database?
... If you just have a handful of genes you can look them up in Ensembl, which hosts dbSNP data.
Go to [Ensembl][1] and search for your gene, e.g. STAR. Click on the results to go to the gene tab and find the [Variant table][2] in the left-hand navigation panel. You can use the filter options above th ...
written 11 weeks ago by
Erin_Ensembl • 280
2
votes
3
answers
194
views
3
answers
... You can search for your gene in [Expression atlas][1], where you can see its basal expression and it's expression in certain experimental conditions.
[1]: https://www.ebi.ac.uk/gxa/home ...
written 11 weeks ago by
Erin_Ensembl • 280
2
votes
1
answer
199
views
1
answers
Answer:
A: How to compare two proteomes
... Sounds to me like you just want to find (or rather exclude) orthologues of protein coding genes between a vertebrate species and drosophila.
You can do this across the whole genome in Ensembl's [BioMart][1] - video tutorial [here][2].
Step 1: Choose Ensembl Genes as your database, then choose a ...
written 11 weeks ago by
Erin_Ensembl • 280
0
votes
1
answer
172
views
1
answers
Comment:
C: ID and Variants in VCF
... Yes that looks correct to me! ...
written 11 weeks ago by
Erin_Ensembl • 280
0
votes
2
answers
194
views
2
answers
Comment:
C: MAF format help
... I'm not sure... it may refer to a super contig (long stretch of sequence not yet assembled into chromosomes). Or a part of an alternate assembly (i.e. not part of the main chromosome level assembly, a haplotypic region). I don't know what 'DroPer1' is so I can't really comment further. ...
written 12 weeks ago by
Erin_Ensembl • 280
Latest awards to Erin_Ensembl
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: Fasta file and GTF file for STAR alignment
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Fasta file and GTF file for STAR alignment
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Fasta file and GTF file for STAR alignment
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Fasta file and GTF file for STAR alignment
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1829 users visited in the last hour