User: haiying.kong

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haiying.kong120
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Posts by haiying.kong

<prev • 84 results • page 1 of 9 • next >
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How to find number of genes in Agilent Protocol
... I would like to find out how many genes are in the targeted area for a given Agilent protocol for WES. Agilent website gives only the number of probes, and among the dataset I downloaded, there is one txt file, like: S07604624_Targets.txt gives a list of names. But the list of names is mixture of ge ...
wes written 49 minutes ago by haiying.kong120 • updated 29 minutes ago by genomax226k
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Answer: A: MutSigCV input files
... To get categ for the mutations, I interpreted the terms as CpG: reference allele C/G with adjacent G/C. C:G: reference allele base pair CG A:T: reference allele base pair AT For the coverage data, I removed all mutations with value "null" for "effect". As the instruction on the website: http://soft ...
written 4 weeks ago by haiying.kong120
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MutSigCV input files
... On the document for MutSigCV: http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV I know you can use the datasets come along with the software, but it is not going to be the best if you can provide details from your own data. So I am trying to provide information fr ...
software written 4 weeks ago by haiying.kong120
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Threshold for WES low coverage proportion
... For WES data, I calculated the proportion of bases with no coverage within target region. What threshold can I set the decide if the sample is good or poor? ...
wes written 5 weeks ago by haiying.kong120
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Comment: C: What does Entrez_Gene_Id 0 mean?
... For an intergenic mutation, there should not be gene symbol, and it cannot be classified as missense mutation. But some of these mutations with Entrez_Gene_Id=0 do have gene symbols and are classified as missense mutation. ...
written 6 weeks ago by haiying.kong120
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What does Entrez_Gene_Id 0 mean?
... I used Oncotator to annotate somatic mutations identified with MuTect2. I found that on the column "Entrez_Gene_Id", there are rows with value "0". I checked these rows, some of them actually have gene symbols and amino acid changes, and are classified as missense mutation. Then there should be a v ...
annotation written 6 weeks ago by haiying.kong120
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Installation of Bioconductor package: lpsymphony
... we are trying to install lpsymphony in a local installation of R-3.3.2. A large part of the build process runs without problems, but at some point the build process ends with a linker error: ... g++ -I/home/kong/lib/R-3.3.2/include -DNDEBUG -ISYMPHONY/include -I/usr/local/include -fpic -g -O2 ...
bioconductor written 6 weeks ago by haiying.kong120 • updated 3 days ago by Biostar ♦♦ 10
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Comment: C: Protein Change Annotation from Oncotator
... Thank you for your reply. I think I was wrong. The software probably did right. But I am looking at BRAF one of the most studied genes. There are some strange protein changes, and if the strand is wrong, it can be explained. But as you said the strand is not wrong. What could be the problem? the pr ...
written 10 weeks ago by haiying.kong120
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Protein Change Annotation from Oncotator
... I ran oncotator on MuTect2 output. I found that the strand is not taken in consideration when protein change is decided. For instance, if the SNV is G>A on negative strand, on positive strand it should be C>T, and when we decide the protein change, we should consider C>T, bot G>A. ...
oncotator written 10 weeks ago by haiying.kong120 • updated 10 weeks ago by Vivek1.6k
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Comment: C: QC for Whole Exome Sequence Data
... Thank you very much for your reply. So how uniform the coverage is should not be a standard to decide if the data for the sample is usable or not, right? I think as long as the proportion of low coverage base is under control, how uniform the coverage is should not be a problem. ...
written 3 months ago by haiying.kong120

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