User: c.clarido

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c.clarido50
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Location:
Netherlands/Rotterdam/Leiden University (Applied Science)
Last seen:
2 weeks, 3 days ago
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2 years ago
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Posts by c.clarido

<prev • 50 results • page 1 of 5 • next >
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Comment: C: VEP specific celltype defining regulatory variants
... I am using vep96 and it's not there, probably this is from the newer version. I will try to update my cache file. Thank you very much for the help! ...
written 26 days ago by c.clarido50
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Comment: C: VEP specific celltype defining regulatory variants
... Hello Emily, We are using GRCh38 ...
written 26 days ago by c.clarido50
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Answer: A: VEP specific celltype defining regulatory variants
... Thank you for the reply, I am not very familiar with the regulatory Ensembl build, however [here][1] they list the sources they used in the build, which includes melanocyte cell line (foreskin melanocyte) from Roadmap epigenomics. How come this is not on the list? How is the --regulatory flag conn ...
written 26 days ago by c.clarido50
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VEP specific celltype defining regulatory variants
... Hello biostar community, I was just wondering if it is possible to have VEP report regulatory region in melanoma or melanocyte specific cell line? I tried to list the avaialble celltypes in vep96, however none of above mentioned celllines were there PC_3 PC_9 Pancreas Placenta ...
ensembl celltype vep regulatory written 27 days ago by c.clarido50
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Comment: C: VEP: filter_vep, custom VCF annotation (kaviar)
... Hello, actually kaviar had variants with multiple allele ...
written 27 days ago by c.clarido50
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Comment: C: VEP: filter_vep, custom VCF annotation (kaviar)
... Hello Emily, Thank you for the quick response. I used the --custom as follow: --custom ~{kaViarPath},kaviar,vcf,exact,0,AF wouldn't it have matched only the exact coordinates? ...
written 4 weeks ago by c.clarido50
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VEP: filter_vep, custom VCF annotation (kaviar)
... Hello biostars community, I have recently annotated a multi-sample VCF using VEP standalone with plugins and custom annotations. For custom annotations, I used kaviar, goNl and gnomAD. After annotation, I wanted to filter rare damaging missense variants. At this moment I have the following fil ...
kaviar filter_vep vep written 4 weeks ago by c.clarido50 • updated 4 weeks ago by Emily_Ensembl19k
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Comment: C: FANTOM5 enhancers: intepretations
... Thank you Kevin! > I assume that 'TCs' refers to 'tag clusters'; so, the higher the > number, the greater the activity of the enhancer region. Do we look at the last column or the 4th column for scores? and are there any cut-offs? ...
written 3 months ago by c.clarido50
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FANTOM5 enhancers: intepretations
... Hello community, I have recently downloaded a melanocyte-specific FANTOM5 Human Enhancer Tracks (http://slidebase.binf.ku.dk/human_enhancers/presets). The fist 4 lines of the bed file looks like this: chr1 1014834 1015095 chr1:1014834-1015095 0.034 . 1014858 1014859 0,0,0 2 ...
fantom5 enhancers written 3 months ago by c.clarido50 • updated 3 months ago by Kevin Blighe51k
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Comment: C: ensembl VEP: gnomAD genome annotation <AF1>&<AF2>
... yes sir: rs868804354 ...
written 4 months ago by c.clarido50

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