User: mangfu100
mangfu100 • 730
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Posts by mangfu100
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6
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1.8k
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... 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? ...
2
votes
1
answer
762
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1
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... 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 ...
4
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1
answer
1.6k
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1
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... 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 ...
0
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1
answer
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1
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... 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 ...
written 4.5 years ago by
mangfu100 • 730
• updated
4.5 years ago by
Pierre Lindenbaum ♦ 129k
0
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0
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... 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 ...
written 4.7 years ago by
mangfu100 • 730
1
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0
answers
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... 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 ...
written 4.7 years ago by
mangfu100 • 730
• updated
4.7 years ago by
Istvan Albert ♦♦ 84k
0
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1
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1.4k
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1
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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 4.9 years ago by
mangfu100 • 730
0
votes
1
answer
1.4k
views
1
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... 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? ...
written 4.9 years ago by
mangfu100 • 730
• updated
4.9 years ago by
Chirag Nepal • 2.2k
1
vote
0
answers
1.4k
views
0
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... 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 ...
written 4.9 years ago by
mangfu100 • 730
0
votes
1
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5.9k
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1
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... Thanks you.
The packages you made will be helpful in my research. I will use it later :)
...
written 5.0 years ago by
mangfu100 • 730
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