User: mangfu100

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mangfu100710
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Korea, Republic Of
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2 years, 7 months ago
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Posts by mangfu100

<prev • 134 results • page 1 of 14 • next >
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Difference between somatic mutations and somatic hyper mutation
... Hi all. I am having a question about some terminologies. I know what the somatic mutations. However, what is the hyper mutations? Is there any distinct difference between them? ...
sequencing written 3.3 years ago by mangfu100710 • updated 3.3 years ago by Dan Gaston7.1k
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Terminologies about hyper mutation
... Hi all. I am having a question about hyper mutations. While I am reading a paper (http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html) the terminology (localized substitution hypermutations) is something strange to me. Even though I searched it on the Internet, but I failed to f ...
sequencing written 3.3 years ago by mangfu100710 • updated 3.3 years ago by Dan Gaston7.1k
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Questions about CpG concept
... Hi all. I am reading a paper but I couldn't understand some concepts even though I tried to search it on the web. here is the paper's address and in the article, below bold sentence is what I didn't understand. (http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html) **Both are c ...
sequencing written 3.3 years ago by mangfu100710 • updated 3.3 years ago by kloetzl1.0k
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How to calculate read depth and coverage for whole exome sequencing?
... Hi all. I am struggling to find a tool for extracting the read depth information and sequence coverage. I know their information is very important before variant callings. It is necessary tasks. I found some good tools such as bedtools and used them to extract what I want.  However, I failed. W ...
next-gen alignment written 3.6 years ago by mangfu100710 • updated 3.6 years ago by Pierre Lindenbaum122k
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genomic characteristics between copy number gain and loss
... Hi all. I analyzed the copy number variations detected from bladder cancer. While analyzing them, I found that the patterns of copy number gain and copy number loss are totally different by the fact that the length of each cnv segment are different.  In general, copy number gain has short high le ...
genome sequencing written 3.8 years ago by mangfu100710
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Question about FIELD information in samtools
... Hi all. I am using the samtools to annotate my variants information and also am trying to use the I16 Field provided by samtools. you can see its manual at http://samtools.sourceforge.net/mpileup.shtml There are a total of 16 independent values in I16 field and first one is "#reference Q13 bases ...
next-gen sequence sequencing written 3.8 years ago by mangfu100710 • updated 3.8 years ago by Istvan Albert ♦♦ 81k
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Comment: C: Question about mutation spectrum
... Thanks for your reply. To better understand, let me give an example. the number of C->T mutations is 5 and the number of G->A mutations is 11. than C:G->T:A is 16. Is that right? ...
written 4.0 years ago by mangfu100710
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Question about mutation spectrum
... Hi all. I am wondering how to calculate the mutation spectrum. In paper, I found notations below which seem to refer the mutation spectrum. C:G-> G:C C:G -> T:A C:G -> A:T (I skipped the all of the notations due to space) My questions is as below. 1. How to interpret notation above? ...
genome next-gen sequencing written 4.0 years ago by mangfu100710 • updated 4.0 years ago by Chirag Nepal2.2k
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how to normalize chromosome arms?
... Hi all. I have some questions regarding the distribution of copy number variations. while. reading some papers, I found that they often grouped the CNVs according to its size. As shown in figure a, this paper used a normalized chromosome arms to separate focal and arm-level SCNVs. However, I d ...
sequence next-gen written 4.0 years ago by mangfu100710
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Comment: C: how to make this plot for mutation?
... Thanks you. The packages you made will be helpful in my research. I will use it later :) ...
written 4.1 years ago by mangfu100710

Latest awards to mangfu100

Popular Question 2.8 years ago, created a question with more than 1,000 views. For how to make this plot for mutation?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to get mutation frequency from exome sequencing data?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to interpret mutation mapper in CBioportal for mutation?
Student 2.8 years ago, asked a question with at least 3 up-votes. For What is your preferred annotation techniques when you analyze mutation in exome seq?
Great Question 3.3 years ago, created a question with more than 5,000 views. For What is difference between soft-clipped and hard-clipped in SAM specification?
Great Question 3.3 years ago, created a question with more than 5,000 views. For What is SIFT-score?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For What is difference between soft-clipped and hard-clipped in SAM specification?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Fusion with strand orientation
Popular Question 3.3 years ago, created a question with more than 1,000 views. For how to make this plot for mutation?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Why does the BLAST use E-value instead of p-value?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Question about Somatic and Germline with homozygous and heterozygous
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Copy number variation detection tools within exome sequencing
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to get mutation frequency from exome sequencing data?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to check the bam file of read quality with graphically visual?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Curious about gene fusion in exome seuquencing data.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Human dna reference file with no prefix 'chr'
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Curious about gene fusion in exome seuquencing data.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For A simple question regarding homozygous and heterozygous variation.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Question about Somatic and Germline with homozygous and heterozygous
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Question about Somatic and Germline with homozygous and heterozygous
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How to download DNA sample files in dbGap?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For What is difference between soft-clipped and hard-clipped in SAM specification?
Student 3.8 years ago, asked a question with at least 3 up-votes. For What is your preferred annotation techniques when you analyze mutation in exome seq?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For What is difference between soft-clipped and hard-clipped in SAM specification?

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