User: haiying.kong
haiying.kong • 340
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Posts by haiying.kong
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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.kong • 340
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... 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?
...
written 4 weeks ago by
haiying.kong • 340
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... 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.kong • 340
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... 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.kong • 340
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... 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 ...
written 4 weeks ago by
haiying.kong • 340
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... > 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) ...
written 4 weeks ago by
haiying.kong • 340
• updated
4 weeks ago by
GenoMax ♦ 96k
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... 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? ...
written 4 weeks ago by
haiying.kong • 340
11
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5 follow
1
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... 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 ...
written 2.9 years ago by
haiying.kong • 340
• updated
2.9 years ago by
Damian Kao ♦ 15k
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... 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.kong • 340
3
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766
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6 follow
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... I found structural variations from WES data. The top frequency genes are almost all pseudogenes.
Could anyone please give me any advice? ...
written 2.9 years ago by
haiying.kong • 340
• updated
2.9 years ago by
d-cameron • 2.3k
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