User: German.M.Demidov

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Posts by German.M.Demidov

<prev • 302 results • page 1 of 31 • next >
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Comment: C: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With G
... sure, usually regions in some area around the probe is also covered with reads and may be efficiently used for SNVs detection, some people use 200 bp, some people calculate effective enrichment looking at the results instead of provided regions file ...
written 1 day ago by German.M.Demidov1.5k
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Comment: C: VCF comparison: shared variants
... You can try this tool: https://github.com/imgag/ngs-bits/blob/master/doc/tools/SampleSimilarity/index.md ...
written 2 days ago by German.M.Demidov1.5k
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Comment: C: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With G
... I'd use any of them + 100bp to the left and to the right ...
written 2 days ago by German.M.Demidov1.5k
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... I did this and I found the same and I was not surprised or confused - that's how statistics works and most of the CNV-detection tools in NGS are based on statistical methods ...
written 3 days ago by German.M.Demidov1.5k
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... I am not sure I understand, but may be the problem you describe is called "random sampling" ...
written 4 days ago by German.M.Demidov1.5k
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... Which tool do you use? ...
written 4 days ago by German.M.Demidov1.5k
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Comment: C: Missing SNPs in sequencing.com from BAM file
... I went through the same steps with my friend who is a programmer and not a bioinformatician like, during last month =) yeap, there are a lot of problems. I'll try to answer your questions once I'll have some time. In a meanwhile, if you have a lot of computational resources, you can try https://git ...
written 8 days ago by German.M.Demidov1.5k
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Comment: C: Missing SNPs in sequencing.com from BAM file
... oh. I've posted it, but have not added links since the third chapter was quite controversial. It is here https://medium.com/@german.m.demidov/how-to-analyse-your-own-dna-a-point-of-view-of-ordinary-customer-part-ii-dc558557db36 . Plan to add "bioinfo" part and others, but it goes into a shaky ground ...
written 8 days ago by German.M.Demidov1.5k
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Answer: C: How to smooth methylation data
... There are many papers that use smoothing as a first step of their approach, such as: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-10-r83 , I think you may check which approach they have applied. ...
written 8 days ago by German.M.Demidov1.5k
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Comment: C: Detection of CNV(InDel) of intermediate size
... The answers are yes to all these questions :) thing get much easier when we switch to wgs, but in Wes we have a blind spot between approx 100bp to 4 kb of coding part variants. ...
written 13 days ago by German.M.Demidov1.5k

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Popular Question 11 days ago, created a question with more than 1,000 views. For NGSchool: Central European School in Bioinformatics
Commentator 20 days ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 28 days ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Commentator 29 days ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 12 weeks ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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Scholar 4 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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Appreciated 4 months ago, created a post with more than 5 votes. For ClinCNV: CNV detection from short reads
Scholar 4 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders
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Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 2.2 years ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
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