User: Ming Tang

gravatar for Ming Tang
Ming Tang2.5k
Reputation:
2,460
Status:
Trusted
Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
1 month, 1 week ago
Joined:
5 years, 11 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 • 299 results • page 1 of 30 • next >
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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 6 weeks 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 15 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 15 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 15 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 15 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 15 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 15 months ago by Ming Tang2.5k • updated 15 months ago by Alex Reynolds28k
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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 15 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 18 months ago by Ming Tang2.5k
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Comment: C: indel preprocessing prior to bam-readcount
... chr12 46236017 . CA C for bam-readcount, you need to supply chr12 46236018 46236018 as the position ...
written 18 months ago by Ming Tang2.5k

Latest awards to Ming Tang

Appreciated 4 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 4 months ago, created a question with more than 1,000 views. For merge structural variant calls in bedpe format
Great Question 4 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Great Question 5 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Popular Question 9 months ago, created a question with more than 1,000 views. For merge structural variant calls in bedpe format
Popular Question 9 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Popular Question 13 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Great Question 13 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Appreciated 15 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 16 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Student 18 months ago, asked a question with at least 3 up-votes. For what is the fastest way to sort big bam files? (300Gb)
Popular Question 18 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Appreciated 19 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 19 months ago, created a question with more than 1,000 views. For any tutorials for structural variants filtering and prioritization
Popular Question 19 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 19 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Popular Question 20 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 21 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For what tools to visualize structural variants VCF files?
Popular Question 21 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 22 months ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Appreciated 23 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison

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