User: haiying.kong

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haiying.kong170
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Location:
Germany
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1 month, 3 weeks ago
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2 years, 2 months ago
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Posts by haiying.kong

<prev • 107 results • page 1 of 11 • next >
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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 8 weeks ago by haiying.kong170
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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 8 weeks ago by haiying.kong170
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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 8 weeks ago by haiying.kong170
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Comment: C: Sample contamination level over 30%
... I am asking for someone else. Because I saw it published on IF 5+ journal. They did not mention contamination level,. ...
written 8 weeks ago by haiying.kong170
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Comment: C: Sample contamination level over 30%
... No, that is not the point! My point is not how to find contamination level. Assuming the computation is correct! Then if a tumor sample has such high level of contamination, can I still use any findings from the sample? The sample is WES, and if I validate with extra experiment on other samples fo ...
written 8 weeks ago by haiying.kong170
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Comment: C: Sample contamination level over 30%
... run ContEst in GATK tools ...
written 8 weeks ago by haiying.kong170
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Comment: C: Sample contamination level over 30%
... cross-individual contamination. ...
written 8 weeks ago by haiying.kong170
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Sample contamination level over 30%
... I have a pair of samples (normal and blood) that are whole exome sequenced. I checked contamination level of the samples. Tumor is contaminated at level of 30%. If I do validation experiment for any findings from this pair of samples, can I get my work published? ...
next-gen written 8 weeks ago by haiying.kong170
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OncodriveFML --- ERROR:root:Impossible to download.
... When I run the sample command line with sample data for OncodriveFML, I got the error message: (OncodriveFML) kong@cloud-hpc-06-kong:~/Haiying/Projects/PrimaryMelanoma/temp> oncodrivefml -i paad.txt.gz -e cds.regions.gz --type coding --sequencing wes -c oncodrivefml.conf ERROR:root:Impossible to ...
oncodrivefml written 5 months ago by haiying.kong170
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Answer: A: Main title on RCircos plot
... functions locator and text can do the job. ...
written 5 months ago by haiying.kong170

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