User: Ming Tang

gravatar for Ming Tang
Ming Tang2.3k
Reputation:
2,290
Status:
Trusted
Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
2 days, 15 hours ago
Joined:
5 years, 1 month 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 • 298 results • page 1 of 30 • next >
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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 5 months ago by Ming Tang2.3k
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Comment: C: bedops -u does not work properly
... it is under-appreciated compared with bedtools, another good one :) ...
written 5 months ago by Ming Tang2.3k
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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 5 months ago by Ming Tang2.3k
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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 5 months ago by Ming Tang2.3k
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Comment: C: bedops -u does not work properly
... even version: 2.4.30 (typical) is having the same issue. ...
written 5 months ago by Ming Tang2.3k
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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 5 months ago by Ming Tang2.3k • updated 5 months ago by Alex Reynolds24k
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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 5 months ago by Ming Tang2.3k
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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 8 months ago by Ming Tang2.3k
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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 8 months ago by Ming Tang2.3k
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Comment: C: How to convert bam-readcount output to BED-VAF format
... for 2 91950203 88 A -A,C,+C 86 1,1,3 why ALT_DP + REF_DP != TOTAL_DP? 86 + 1 + 1 + 3 =91 not 88? Thanks! ...
written 8 months ago by Ming Tang2.3k

Latest awards to Ming Tang

Popular Question 3 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Great Question 3 months ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Appreciated 5 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 6 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Student 8 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 8 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Appreciated 9 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 9 months ago, created a question with more than 1,000 views. For any tutorials for structural variants filtering and prioritization
Popular Question 9 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 9 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Popular Question 10 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 11 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For what tools to visualize structural variants VCF files?
Popular Question 11 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 12 months ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
Appreciated 13 months ago, created a post with more than 5 votes. 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
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Appreciated 13 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Great Question 14 months ago, created a question with more than 5,000 views. For htseq-count for pair-end RNA-seq
Popular Question 14 months ago, created a question with more than 1,000 views. For what is the fastest way to sort big bam files? (300Gb)
Popular Question 14 months ago, created a question with more than 1,000 views. For what is the fastest way to sort big bam files? (300Gb)
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments

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