User: haiying.kong

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haiying.kong340
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Germany
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Posts by haiying.kong

<prev • 126 results • page 1 of 13 • next >
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Comment: C: Reference genome for CIViC data
... Thanks a lot. Yes, it says hg37. I was trying to find the information from webstie. ...
written 4 weeks ago by haiying.kong340
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Reference genome for CIViC data
... I am trying to use the dataset on from the website: https://civicdb.org/releases For the summary tables, there is information that the data is with hg37 as reference genome. But for vcf files, no where is saying anything about reference genome. Are they all still using hg37 as reference? ...
database written 4 weeks ago by haiying.kong340
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Comment: C: GATK Funcotator missing DP and AF information from vcf file
... In addition to GATK folks, people all over around world who are using Funcotator. If some of them have encountered similar problems and resolved it, then they could help me. Your claim is valid only if for one post, only one response is needed to be efficient. The reality is that people could give ...
written 4 weeks ago by haiying.kong340
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Comment: C: GATK Funcotator missing DP and AF information from vcf file
... this post is different. The previous one is talking about Variant_Classification mistaken missense to intron. This one is talking about maf file could not catch the information in vcf file about DP and AF only for some variants. You make me feel stalked. ...
written 4 weeks ago by haiying.kong340
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GATK Funcotator missing DP and AF information from vcf file
... I have posted a post on GATK forum. Please help me. https://gatk.broadinstitute.org/hc/en-us/community/posts/360076880272-GATK-Funcotator-missing-DP-and-AF-information-from-vcf-file ...
software error written 4 weeks ago by haiying.kong340
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GATK Funcotator Variant_Classification
... > If you are seeing an error, please provide(REQUIRED) : a) GATK > version used: b) Exact command used: c) Entire error log: > > If not an error, choose a category for your question(REQUIRED): a)How > do I (......)? b) What does (......) mean? c) Why do I see (......)? > d) ...
annotation for mutation written 4 weeks ago by haiying.kong340 • updated 4 weeks ago by GenoMax96k
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How to download as table from mycancergenome
... I would like to download in table format for the list of biomarkers on the website: https://www.mycancergenome.org/content/biomarkers/#biomarker_type=Gene I cannot find any option for downloading. Could anyone please help me? ...
database written 4 weeks ago by haiying.kong340
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KEGGREST -- gene list
... library(KEGGREST) > names(keggGet("map07049")[[1]]) [1] "ENTRY" "NAME" "PATHWAY_MAP" "COMPOUND" "REFERENCE" I need to get gene list (hugo-symbol) in each pathway. How can I get this from KEGGREST? > sessionInfo() R version 3.3.3 (2017-03-06) Platf ...
R keggrest bioconductor written 2.9 years ago by haiying.kong340 • updated 2.9 years ago by Damian Kao15k
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Comment: C: Do structural variations on pseudo-gene mean any thing?
... Thank you very much for your reply. I have whole exome sequence data from matched blood and tumor samples, used Mirkat to identify somatic structural variations, then annotated them with gene names. ...
written 2.9 years ago by haiying.kong340
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Do structural variations on pseudo-gene mean any thing?
... I found structural variations from WES data. The top frequency genes are almost all pseudogenes. Could anyone please give me any advice? ...
biology written 2.9 years ago by haiying.kong340 • updated 2.9 years ago by d-cameron2.3k

Latest awards to haiying.kong

Appreciated 22 months ago, created a post with more than 5 votes. For .dict file created by picard and by samtools
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