User: Abdel
Abdel • 150
- Reputation:
- 150
- Status:
- New User
- Location:
- Montreal
- Last seen:
- 9 years, 1 month ago
- Joined:
- 9 years, 9 months ago
- Email:
- d*******@msn.com
Junior Bioinformatician Montreal Heart institute (Pharmacogenomics center)
Posts by Abdel
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... that is a great resource !
I'm tring to use the Perl API ...i installed the `Webservice::InterMine`, but I get this error when I execute a template script. Any idea?
```
Error
Error
FW-1 at tornado: Access denied.
``` ...
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... Hi all
when i give this snp (6 7526000 7526000 C A) to annovar (hg18)
it is supposed to give me two isoforms(for DSP gene) in the results but it doesn't !
nonsynonymous SNV DSP:NM_004415:exon23:c.C4578A:p.N1526K
any explanation ?
...
written 9.3 years ago by
Abdel • 150
• updated
9.3 years ago by
Larry_Parnell ♦ 16k
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... Hi All
which is the best database choice from where i can extract a data set of causative variants and a data set of benign variants (OMIM ,GWAS).
Thanks
...
written 9.3 years ago by
Abdel • 150
• updated
9.3 years ago by
Larry_Parnell ♦ 16k
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... Hi folks
I m trying to find a way to get the phyloP score for a given physical position , i tried to query the ucsc sql phyloP46wayPlacental table , but i realized that the score I'm looking after is not present in the table .
If anybody have an idea of how to get the mean score , let me know ple ...
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... Thanks Jorge that was helpfull ...
written 9.5 years ago by
Abdel • 150
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... It seems like a really powerfull tool , i'm interested on the stand alone version , it take a lot of time to prepare all the stuff , but i'll try it...i was wondering if it works with novel variant (no rs) ? ...
written 9.5 years ago by
Abdel • 150
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... Hi everybody
I have a large set of variant , i have to get allele frequency of CEU,YRI and JPT populations from 1000 genome , dbsnp132 and hapmap .
I simply don't know where to begin....should I download all 1000 genome ,dbsnp and HAPMAP database ?
what files should I download ? there is lot of ...
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... if i'm not mistaken , the phyloP score for the chr1 10918 is 0.064
it is intuitive , the confusing thing is that when querying ucsc table browser for this position ,i found a different value 0.0400079
(clade :mammal ,Group :comparative genomics ,track :conservation ,table :mammals Cons phyloP46wayP ...
written 9.6 years ago by
Abdel • 150
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... if i'm not mistaken , the phyloP score for the chr1 10918 is 0.064
it is intuitive , the confusing thing is that when querying ucsc table browser for this position ,i found a different value 0.0400079
(clade :mammal ,Group :comparative genomics ,track :conservation ,table :mammals Cons phyloP46wayP ...
written 9.6 years ago by
Abdel • 150
6
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... Hi everyone
I downloaded the chr1.phyloP46way.placental.wigFix file from ucsc , i need it to get a phyloP score for a given position of the chr1 .
My problem is that there is no position field in this file , just the scores...
0.056
0.056
0.056
0.064
0.056
0.064
0.056
.
.
.
Did someone ...
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