User: Ming Tang
Ming Tang • 2.6k
- Reputation:
- 2,640
- Status:
- Trusted
- Location:
- Houston/MD Anderson Cancer Center
- Website:
- http://crazyhottommy.b...
- Twitter:
- @tangming2005
- Last seen:
- 1 month, 1 week ago
- Joined:
- 7 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
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... you can call peaks from bedgraph using:
macs2 bdgpeakcall
usage: macs2 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g MAXGAP]
[--cutoff-analysis] [--no-trackline]
[--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)
macs2 bdgpeakcall: error: the ...
written 8 weeks ago by
Ming Tang • 2.6k
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1
answer
498
views
1
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... under the run: indent the if statement. ...
written 8 months ago by
Ming Tang • 2.6k
1
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1
answer
8.1k
views
1
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... was googling something else and found this...thanks Vivek for promoting my blog.
I now blog at https://divingintogeneticsandgenomics.rbind.io/ :) ...
written 20 months ago by
Ming Tang • 2.6k
1
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... 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 22 months ago by
Ming Tang • 2.6k
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1
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776
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1
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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 3.0 years ago by
Ming Tang • 2.6k
0
votes
1
answer
776
views
1
answers
Comment:
C: bedops -u does not work properly
... it is under-appreciated compared with bedtools, another good one :) ...
written 3.0 years ago by
Ming Tang • 2.6k
0
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1
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776
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1
answers
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 3.0 years ago by
Ming Tang • 2.6k
0
votes
1
answer
776
views
1
answers
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 3.0 years ago by
Ming Tang • 2.6k
0
votes
1
answer
776
views
1
answers
Comment:
C: bedops -u does not work properly
... even version: 2.4.30 (typical) is having the same issue. ...
written 3.0 years ago by
Ming Tang • 2.6k
4
votes
1
answer
776
views
1
answer
... 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 ...
written 3.0 years ago by
Ming Tang • 2.6k
• updated
3.0 years ago by
Alex Reynolds ♦ 31k
Latest awards to Ming Tang
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Peak callers for ChIP seq comparison
Great Question
5 months ago,
created a question with more than 5,000 views.
For RNAseq heatmap.2 log2FC clustering
Popular Question
14 months ago,
created a question with more than 1,000 views.
For merge structural variant calls in bedpe format
Appreciated
14 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 RNAseq heatmap.2 log2FC clustering
Popular Question
14 months ago,
created a question with more than 1,000 views.
For MACS2 reads report inconsistent with samtools flagstat
Epic Question
14 months ago,
created a question with more than 10,000 views.
For K-Means Clustering And Heatmap
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Identification of functionally relevant regions from ChIP-seq experiments
Scholar
15 months ago,
created an answer that has been accepted.
For A: Wig Files- Macs Vs. Igvtools Count In Focal Amplification
Epic Question
17 months ago,
created a question with more than 10,000 views.
For Extract Dendrogram Information From Heatmap Generated By Heatmap.2
Great Question
19 months ago,
created a question with more than 5,000 views.
For RNAseq heatmap.2 log2FC clustering
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: Identification of functionally relevant regions from ChIP-seq experiments
Great Question
2.1 years ago,
created a question with more than 5,000 views.
For RNAseq heatmap.2 log2FC clustering
Appreciated
2.1 years ago,
created a post with more than 5 votes.
For A: Peak callers for ChIP seq comparison
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For merge structural variant calls in bedpe format
Great Question
2.2 years ago,
created a question with more than 5,000 views.
For RNAseq heatmap.2 log2FC clustering
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For merge structural variant calls in bedpe format
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For convert SNP calls to amino acid change
Good Answer
2.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Peak callers for ChIP seq comparison
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For convert SNP calls to amino acid change
Good Answer
2.9 years ago,
created an answer that was upvoted at least 5 times.
For A: Peak callers for ChIP seq comparison
Great Question
2.9 years ago,
created a question with more than 5,000 views.
For RNAseq heatmap.2 log2FC clustering
Appreciated
3.0 years ago,
created a post with more than 5 votes.
For A: Peak callers for ChIP seq comparison
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For convert SNP calls to amino acid change
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