User: Sharon

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Sharon30
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Posts by Sharon

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Rare variant analysis
... OK, Got it. Many thanks ...
written 9 days ago by Sharon30
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Comment: C: Rare variant analysis
... I think I did not clarify my question correctly. So, when they say 'this given approach works when variants have the same direction', by same direction they mean all variants are risk increasing or all variants are risk decreasing? ...
written 10 days ago by Sharon30
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Rare variant analysis
... I started doing some rare variant association analysis tests like burden tests and other types. Some methods say whether it suits risk-increasing and risk-decreasing variants . I don't understand what is the meaning of risk increasing versus risk decreasing variants? Thanks ...
rare variants written 10 days ago by Sharon30 • updated 10 days ago by WouterDeCoster22k
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Answer: A: Tophat alignments is low but STAR is high.
... I think also I am using the default parameters of Star which could be the reason for the difference. 10 mismatches in Star vs 2 only in tophat. Also the softclipping default is high in Star vs no in tophat. ...
written 12 days ago by Sharon30
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Tophat alignments is low but STAR is high.
... If I used Tophat to align reads to human genome and I got ~72% alignment rate. Then I realigned the reads using STAR and around 90% of the reads were mapped. I also used the same commands of tophat to align another dataset and got 90% alignments rate. So I don't think I am not using tophat incorre ...
alignment rna-seq written 12 days ago by Sharon30
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Comment: C: Runs of homozygosity
... Got it. Thanks so much. Many thanks ...
written 14 days ago by Sharon30
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Comment: C: Runs of homozygosity
... Thank you. It would help me more if you can give me an example of ROH with allelic match versus without allelic match? ...
written 15 days ago by Sharon30
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Runs of homozygosity
... What does overlapping ROH with allelic match mean as defined in plink? I mean what we can tell from overlapping ROH with/without allelic match? Does this refer to anything to kinship relatedness? Like if we have two persons who have long overlapping ROH with allelic match, does this mean they are po ...
roh plink overlapping roh written 16 days ago by Sharon30 • updated 15 days ago by Kevin Blighe3.4k
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Comment: C: Exac and gnomad MAF value in VCF
... Got it, thanks all so much ! ...
written 16 days ago by Sharon30
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Comment: C: Exac and gnomad MAF value in VCF
... I understand the difference between zero and null in computer science/software engineering, that's not my question. I mean zero and null in the variant annotations context. A zero Maf means not found in the population. Null means missing. What is the difference between not found and missing. Examp ...
written 16 days ago by Sharon30 • updated 16 days ago by Pierre Lindenbaum99k

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