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User: tangming2005

gravatar for tangming2005
tangming2005 • 2.1k
Reputation:
2,070
Status:
Trusted
Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
3 days, 7 hours ago
Joined:
4 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 tangming2005

<prev • 280 results • page 1 of 28 • next >
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Answer: A: How to use the qvalue function for multiple testing?
... read here for some idea http://crazyhottommy.blogspot.com/2015/03/understanding-p-value-multiple.html also type ?qvalue to see some help. ...
written 3 days ago by tangming2005 • 2.1k
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... I started using snakemake 6 months ago, and now I have shifted all my pipelines to snakemake (ChIP-seq, RNA-seq, ATAC-seq and DNA-seq). I am pretty happy with it. once you get the idea of how snakemake works (think in a bottom-up fashion), it is easy to build up your own pipelines. BTW, the document ...
written 4 days ago by tangming2005 • 2.1k
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Comment: C: When and why is bwa aln better then bwa mem?
... answer my own question. I tested using teaser http://teaser.cibiv.univie.ac.at/reports/8dc974f7ce99f6958012619c052e5597/index.html#section4 and bwa aln seems to be a little better than bwa mem for 36bp short single end reads. ...
written 10 days ago by tangming2005 • 2.1k
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Answer: A: Good Pipeline for ChIPexo
... bowtie2 is for reads longer than 50bp if you have short reads such as 36 bp use bowtie1 ...
written 18 days ago by tangming2005 • 2.1k
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Comment: C: Peak calling for broad histone-modification regions
... take a look at epic https://github.com/biocore-ntnu/epic ...
written 5 weeks ago by tangming2005 • 2.1k
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Comment: C: Software for Tree Visualization
... yes https://github.com/GuangchuangYu/ggtree check if it takes your format as input or not. ...
written 5 weeks ago by tangming2005 • 2.1k
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Comment: C: Software for Tree Visualization
... there is a ggtree package you can take a look. ...
written 5 weeks ago by tangming2005 • 2.1k
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Comment: C: Seeking private tutor to learn RNA/ChIP-Seq data analysis
... Thanks for your good words. I will keep up the good work :) ...
written 5 weeks ago by tangming2005 • 2.1k
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Answer: A: Seeking private tutor to learn RNA/ChIP-Seq data analysis
... you can read my github notes to start https://github.com/crazyhottommy both ChIP-seq and RNA-seq are the most stared repos. ...
written 6 weeks ago by tangming2005 • 2.1k
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Answer: A: Depth of coverage in Bam file does not match depth in VCF file
... as Pierre says, most callers do some filtering of the reads, so the reads number in the VCF file will be fewer than in the bam file. ...
written 6 weeks ago by tangming2005 • 2.1k

Latest awards to tangming2005

Popular Question 8 days ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Great Question 10 weeks ago, created a question with more than 5,000 views. For htseq-count for pair-end RNA-seq
Popular Question 11 weeks ago, created a question with more than 1,000 views. For what is the fastest way to sort big bam files? (300Gb)
Popular Question 12 weeks ago, created a question with more than 1,000 views. For what is the fastest way to sort big bam files? (300Gb)
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Popular Question 3 months ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
Epic Question 3 months ago, created a question with more than 10,000 views. For Extract Dendrogram Information From Heatmap Generated By Heatmap.2
Popular Question 5 months ago, created a question with more than 1,000 views. For Macs Chip-Seq Contorl
Popular Question 7 months ago, created a question with more than 1,000 views. For Macs Chip-Seq Contorl
Popular Question 7 months ago, created a question with more than 1,000 views. For Are adapters removed for fastq files dumped from sra from GEO?
Popular Question 8 months ago, created a question with more than 1,000 views. For Are adapters removed for fastq files dumped from sra from GEO?
Popular Question 8 months ago, created a question with more than 1,000 views. For Are adapters removed for fastq files dumped from sra from GEO?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 8 months ago, created a question with more than 1,000 views. For RNAseq heatmap.2 log2FC clustering
Appreciated 9 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Appreciated 9 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 10 months ago, created a question with more than 1,000 views. For RNAseq heatmap.2 log2FC clustering
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Great Question 10 months ago, created a question with more than 5,000 views. For Extract Dendrogram Information From Heatmap Generated By Heatmap.2
Popular Question 10 months ago, created a question with more than 1,000 views. For RNAseq heatmap.2 log2FC clustering
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