User: Ming Tang

gravatar for Ming Tang
Ming Tang2.5k
Reputation:
2,520
Status:
Trusted
Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
3 weeks, 2 days ago
Joined:
6 years, 7 months ago
Email:
t***********@gmail.com

I graduated from a "wet" lab in 2014. in 2012, I became interested in the bioinformatics field, especially the next generation sequencing field. I really love Unix command line, python and R programming languages. Now I am doing a computational biology postdoc at MD Anderson Cancer Center focusing on glioblastoma genomics.

Posts by Ming Tang

<prev • 300 results • page 1 of 30 • next >
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Comment: C: Interesting bioinformatics blogs (2017 edition)
... was googling something else and found this...thanks Vivek for promoting my blog. I now blog at https://divingintogeneticsandgenomics.rbind.io/ :) ...
written 6 months ago by Ming Tang2.5k
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Comment: C: No called peaks from macse 2 and the alignment rate 90%
... load the bam file or bigwig (make it from bam) to IGV, and visually check if there any enrichment in the genome or not. if not, the experiment failed most likely. ...
written 9 months ago by Ming Tang2.5k
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Comment: C: bedops -u does not work properly
... Thanks for the detailed answer. I used `<()` quite a bit as well :) learning to use more BEDOPS. ...
written 23 months ago by Ming Tang2.5k
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Comment: C: bedops -u does not work properly
... it is under-appreciated compared with bedtools, another good one :) ...
written 23 months ago by Ming Tang2.5k
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Comment: C: bedops -u does not work properly
... Now it makes sense. every input bed file should be sorted. with -u it does not give me errors, but just missing many overlapping entries. bedops is a very good tool BTW:) ...
written 23 months ago by Ming Tang2.5k
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Comment: C: bedops -u does not work properly
... yes, you are right. -ec is for checking error. but bedops -u should not expect sorted bed files, right? ...
written 23 months ago by Ming Tang2.5k
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Comment: C: bedops -u does not work properly
... even version: 2.4.30 (typical) is having the same issue. ...
written 23 months ago by Ming Tang2.5k
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bedops -u does not work properly
... bedops -u is not sorting the bed files bedops --version bedops citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract version: 2.4.14 authors: Shane Neph & Scott Kuehn #dummy file: cat my.bed chr1 1 5 peak_1 chr1 2 6 pea ...
bed bedops intersect written 23 months ago by Ming Tang2.5k • updated 23 months ago by Alex Reynolds29k
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Comment: C: Why do I get a weird copy number in the tumour?
... Hi Eric, may I ask how does the call command work? I have segment file output from sequenza. sequenza also gives a purity estimate. I want to scale the segment depth ratio by the tumor purity. The output of sequenaza segments is diff from cnvkit, so I am not sure how to use the call command. Thanks! ...
written 23 months ago by Ming Tang2.5k
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Answer: A: How to convert bam-readcount output to BED-VAF format
... Just for those who has the same problem, this may help https://github.com/sahilseth/bamreadcountr ...
written 2.2 years ago by Ming Tang2.5k

Latest awards to Ming Tang

Scholar 9 weeks ago, created an answer that has been accepted. For A: Wig Files- Macs Vs. Igvtools Count In Focal Amplification
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Depth of coverage
Epic Question 4 months ago, created a question with more than 10,000 views. For Extract Dendrogram Information From Heatmap Generated By Heatmap.2
Great Question 5 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Great Question 12 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Appreciated 12 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 12 months ago, created a question with more than 1,000 views. For merge structural variant calls in bedpe format
Great Question 13 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Popular Question 17 months ago, created a question with more than 1,000 views. For merge structural variant calls in bedpe format
Popular Question 17 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Popular Question 21 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Great Question 21 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Appreciated 23 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 24 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Student 2.1 years ago, asked a question with at least 3 up-votes. For what is the fastest way to sort big bam files? (300Gb)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 2.3 years ago, created a question with more than 1,000 views. For any tutorials for structural variants filtering and prioritization
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Get all the translation start site for human genome

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