User: mangfu100

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mangfu100730
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Korea, Republic Of
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Posts by mangfu100

<prev • 134 results • page 2 of 14 • next >
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how to make this plot for mutation?
... Hi all. I am wondering that the method of drawing plot like below. Can it be done automatically by using visualization tools or do I have to write codes and combine all of the bars and tables in the figure using R?   ...
genome sequencing written 4.7 years ago by mangfu100730 • updated 4.7 years ago by poisonAlien2.8k
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Comment: C: Role of amino-acid change number
... Thanks for your reply. I have a set of nonsynonymous mutations from 10 patients with bladder cancer. Since my cancer type is a very specific subtype of bladder cancer, I focused more on the recurrently mutated gene in my cohort to identify driver mutations and finally I finalized the set of recurr ...
written 4.7 years ago by mangfu100730
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Role of amino-acid change number
... Hi all. I am wondering the meaning of the number of amino-acid change. For example, I found the somatic mutation that has p.P123F. so the amino acid change notation is P123F, indicating that the protein change occurs from P to F. but what does 123 mean? does it refer to iso-form pattern? my fin ...
genome alignment sequencing written 4.7 years ago by mangfu100730 • updated 2.1 years ago by Biostar ♦♦ 20
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Comment: C: comparing amino acid change is useful when analyzing mutations?
... Thanks for your kindly reply. More detail about my questions, I have a set of nonsynonymous muations in cancer and I would like to know their significance for developing tumorous. So, I came up with ideas that comparing my amino-acid changes from my nonsynonymous mutations with that of mutation tha ...
written 4.7 years ago by mangfu100730
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comparing amino acid change is useful when analyzing mutations?
... Hi all. I am wondering that comparing mutation of amino acid change is useful when analyzing mutations? In my opinion,it might give some knowledge that same amino-acid changes can be grouped together and will be a source of identifying driver mutations in targeted cancer. (Of course, mutations at ...
genome alignment sequencing written 4.7 years ago by mangfu100730
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question about a term regarding copy number aberrations and genes involved in these areas.
... Hi all. In copy number analysis, as some of you already know, copy number variations consist of their segment size and amplitude level and genes involved in their regions.  And also, it is obvious that CNVs that occurred in small segment size having few oncogenes might be considered as more import ...
genome next-gen sequencing written 4.7 years ago by mangfu100730
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Ti Tv ratio and their usefulness in exome sequencing
... Hi all. I am a beginner in the bioinformatics and I have some questions. When I read some papers regarding the mutational landscape, nearly all of them described the Ti Tv ratio in terms of mutation spectrum with some pretty figures. Therefore I would like to apply this statistics to my research b ...
genome next-gen sequencing written 4.7 years ago by mangfu100730 • updated 4.7 years ago by Evgeniia Golovina1.0k
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Comment: C: How to get mutation frequency from exome sequencing data?
... Thanks! Your comments will be very helpful in my research. I will try it :) ...
written 4.7 years ago by mangfu100730
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Comment: C: How to get mutation frequency from exome sequencing data?
... Thanks for you reply. Fortunately, I have a bed for the exome sequencing. my bed files are composed of four columns as follows: GENE START END EXON_NAME As you mentioned, is it right to sum up each (END-START) corresponding each exon and then divide them by mutation that I found? ...
written 4.7 years ago by mangfu100730
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Comment: C: How to get mutation frequency from exome sequencing data?
... Thank you for your comments. What I would like to to is a case that # of mutation / per MB. In this case, how to calculate the MB?  Does it simply refer to sum of entire chromosome's length from 1 to 22? (or just considering only exome length?) ...
written 4.7 years ago by mangfu100730

Latest awards to mangfu100

Popular Question 3.4 years ago, created a question with more than 1,000 views. For how to make this plot for mutation?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to get mutation frequency from exome sequencing data?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to interpret mutation mapper in CBioportal for mutation?
Student 3.4 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 3.9 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 3.9 years ago, created a question with more than 5,000 views. For What is SIFT-score?
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?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Fusion with strand orientation
Popular Question 3.9 years ago, created a question with more than 1,000 views. For how to make this plot for mutation?
Popular Question 3.9 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 3.9 years ago, created a question with more than 1,000 views. For Question about Somatic and Germline with homozygous and heterozygous
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Copy number variation detection tools within exome sequencing
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How to get mutation frequency from exome sequencing data?
Popular Question 3.9 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 3.9 years ago, created a question with more than 1,000 views. For Curious about gene fusion in exome seuquencing data.
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Human dna reference file with no prefix 'chr'
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Curious about gene fusion in exome seuquencing data.
Popular Question 4.2 years ago, created a question with more than 1,000 views. For A simple question regarding homozygous and heterozygous variation.
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Question about Somatic and Germline with homozygous and heterozygous
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Question about Somatic and Germline with homozygous and heterozygous
Popular Question 4.4 years ago, created a question with more than 1,000 views. For How to download DNA sample files in dbGap?
Popular Question 4.4 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 4.4 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 4.5 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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