User: Ming Tang

gravatar for Ming Tang
Ming Tang2.4k
Reputation:
2,380
Status:
Trusted
Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
4 weeks ago
Joined:
5 years, 8 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 • 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 12 months ago by Ming Tang2.4k
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Comment: C: bedops -u does not work properly
... it is under-appreciated compared with bedtools, another good one :) ...
written 12 months ago by Ming Tang2.4k
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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 12 months ago by Ming Tang2.4k
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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 12 months ago by Ming Tang2.4k
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Comment: C: bedops -u does not work properly
... even version: 2.4.30 (typical) is having the same issue. ...
written 12 months ago by Ming Tang2.4k
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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 12 months ago by Ming Tang2.4k • updated 12 months ago by Alex Reynolds27k
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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 12 months ago by Ming Tang2.4k
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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 15 months ago by Ming Tang2.4k
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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 15 months ago by Ming Tang2.4k
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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 15 months ago by Ming Tang2.4k

Latest awards to Ming Tang

Great Question 8 weeks ago, created a question with more than 5,000 views. For RNAseq heatmap.2 log2FC clustering
Popular Question 6 months ago, created a question with more than 1,000 views. For merge structural variant calls in bedpe format
Popular Question 6 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Popular Question 10 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Great Question 10 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 convert SNP calls to amino acid change
Student 14 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 15 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Popular Question 16 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 16 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Popular Question 16 months ago, created a question with more than 1,000 views. For any tutorials for structural variants filtering and prioritization
Appreciated 16 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 17 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 17 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For what tools to visualize structural variants VCF files?
Popular Question 18 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 ChIP-seq analysis tutorial
Appreciated 20 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Appreciated 20 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Great Question 21 months ago, created a question with more than 5,000 views. For htseq-count for pair-end RNA-seq

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