User: dora

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dora 90
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Posts by dora

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Genome Coordinates Between Assemblies: Liftover A Snp Array
... @Emily, Does VEP also convert rs numbers (rs#, SNP numbers) from old to new builds? As far as I see, VEP just does conversion for gene IDs or transcripts. ...
written 3.1 years ago by dora 90
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Answer: A: liftOver UCSC and rs number conversion
... @Pierre, thanks. I did use liftRsNumber.py from http://genome.sph.umich.edu/wiki/LiftOver to lift a list of rs numbers (hg18 to hg19, about 400k SNPs from 2010 or earlier), do you think it is normal that all SNPs are unchanged? Along with the latest version of RsMergeArch and SNPHistory. To compare ...
written 3.1 years ago by dora 90
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liftOver UCSC and rs number conversion
... UCSC liftOver can lift genome positions (also chromosomal position) from hg18 to hg19, but it doesn't convert the rs numbers. For rs numbers from old to new builds can also be changed. Is there any way to solve this? ...
liftover; genome build; rs number; written 3.1 years ago by dora 90
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Comment: C: Updating dbSNP rs ids from old SNP data
... that's true. Did you find a way to solve this? ...
written 3.1 years ago by dora 90
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Comment: C: Updating dbSNP rs ids from old SNP data
... @h.mon, liftOver doesn't reflect the rs number changes, right? ...
written 3.1 years ago by dora 90
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Answer: A: Mapping target bisulfite sequencing reads to a reference
... http://www.bioinformatics.babraham.ac.uk/projects/bismark/   ...
written 3.2 years ago by dora 90
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Comment: A: dbSNP minor allele frequency list
... The output would look like: SNP       MinorAllele   Source rs16532      C         1000Genomes rs165323    T         1000Genomes rs3092950  T         1000Genomes ... ...
written 3.2 years ago by dora 90
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dbSNP: minor alleles for a list of SNPs
... I'm looking for minor alleles generated from current 1000 genome project given a list of SNPs. For example, rs16532, its MAF is 0.3898 with C as the minor allele from 1000 genomes. Does anyone know how I can get the minor alleles from 1k genome or dbSNP for a list of SNPs simultaneously? Or where I ...
1000 genome; snp minor allele frequency; written 3.2 years ago by dora 90 • updated 3.2 years ago by trausch1.2k
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Comment: C: How to interpret heterozygosity rate ?
... sorry, then my answer would be the other way around, meaning that almost all of the samples are heterogeneous (This population is substantial heterogeneous and may include a number of ethnic groups). O/w the samples are contaminated. ...
written 3.6 years ago by dora 90
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Answer: A: How to interpret heterozygosity rate ?
... This may suggest that: Only one individual with het 0.2 shows relatively high autosomal heterozygosity deviation.  The inbreeding coefficent rate is mostly 1. Do you mean the values in the last column of the output het file are almost 1? ...
written 3.6 years ago by dora 90

Latest awards to dora

Student 3.1 years ago, asked a question with at least 3 up-votes. For liftOver UCSC and rs number conversion
Scholar 3.6 years ago, created an answer that has been accepted. For A: How to interpret heterozygosity rate ?

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