User: haiying.kong

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haiying.kong190
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Germany
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3 weeks ago
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Posts by haiying.kong

<prev • 114 results • page 1 of 12 • next >
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Then, he will say: You are making excuse to be lazy! ...
written 25 days ago by haiying.kong190
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Thanks for the advice. If I run, there will be no driver genes identified. So nothing can be included in any paper that can be published. Just waste of my time. But I will keep the email anyway. ...
written 25 days ago by haiying.kong190
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Such communication is impossible with such dense head, sorry to say this word. After "because", there will be scientific explanation that involves statistics, and he refuses to hear any bioinformatics, or statistics, or mathematics in any occasion. He is 100000% pure biologist. ...
written 25 days ago by haiying.kong190
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Is epigenetic still hot field?
... It was very hot several years back. Is it still hot field? I feel much is done in this field, and nothing original is coming out. ...
epigenetic written 27 days ago by haiying.kong190 • updated 27 days ago by Devon Ryan76k
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Comment: C: WES -- How come I found 40% mutations intron regions
... Thanks again for your help. It takes very very long to run MuTect even with many cores or nodes. So I do not have time to rerun, because I am trying to finish up soon. Is there any way to do the filtering from MuTect output? ...
written 9 weeks ago by haiying.kong190
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Comment: C: WES -- How come I found 40% mutations intron regions
... Thanks for your reply. > I do not understand: The reason you're likely seeing a lot of results > is because these areas just beyond the exon boundaries will have much > poorer coverage, and thus calling variants is harder. Do you mean in those intron regions captured, the coverage is poor ...
written 9 weeks ago by haiying.kong190 • updated 9 weeks ago by genomax42k
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WES -- How come I found 40% mutations intron regions
... I have WES data from which identified somatic mutations with MuTect2, and annotated with Oncotator. The protocol captures exomes and UTRs, but on my result, over 40% of mutations are annotated as Intron regions. How is this possible? ...
wes somatic mutation written 9 weeks ago by haiying.kong190 • updated 9 weeks ago by andrew.j.skelton734.3k
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Comment: C: Sample contamination level over 30%
... The thing is that there is only one pair of samples, normal and tumor, for this study whole exome sequenced. After identifying interesting mutations, these mutations are validated on larger number of samples with sanger sequencing which is much cheaper than WES. You are right about "appropriate" ven ...
written 4 months ago by haiying.kong190
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Comment: C: Sample contamination level over 30%
... in fact i used ContEST and verifyBamID to estimate contamination. both gave abot 30%. i used same software tested other samples. none are bad at this level. ...
written 4 months ago by haiying.kong190
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Comment: C: Sample contamination level over 30%
... The point is: whatever they find from the contaminated sample is just suggestion for possible finding. All suggested findings are validated on other samples. Does this make the work qualified for publication? ...
written 4 months ago by haiying.kong190

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