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User: tangming2005

gravatar for tangming2005
tangming2005 • 2.1k
Reputation:
2,150
Status:
Trusted
Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
14 hours ago
Joined:
4 years, 3 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 tangming2005

<prev • 288 results • page 1 of 29 • next >
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Comment: C: Peak calling macs vs Homer
... agreed. you should at least post the commands to show what you have tried. ...
written 7 days ago by tangming2005 • 2.1k
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Comment: C: sample order of the freebayes vcf output
... Thank you for the info. but I saw inside speedseq, the filtering script assumes normal comes first and then tumor. https://github.com/hall-lab/speedseq/blob/master/bin/speedseq#L156 That's what confuses me. Tommy ...
written 12 days ago by tangming2005 • 2.1k
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Comment: C: Any advanced and really structured course on Python language or MySql or R or Un
... check this for R and python http://rafalab.github.io/pages/harvardx.html ...
written 12 days ago by tangming2005 • 2.1k
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sample order of the freebayes vcf output
... Hi, I am testing freebayes on tumor/normal pairs. it seems no matter I put normal or tumor bam first on the command line, the sample order of the vcf is random. tumor:F17042956987-KY290-2-WES normal: B17042956985-KY290-2-WES How does freebayes determine the order? mutect does not maintain the or ...
vcf wes freebayes written 12 days ago by tangming2005 • 2.1k
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Comment: C: Download ENCODE Project BED files using REST API
... you might want to try the Encodexplorer http://bioconductor.org/packages/release/bioc/html/ENCODExplorer.html ...
written 25 days ago by tangming2005 • 2.1k
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Answer: A: Downloading genomic interval for hg38
... see http://crazyhottommy.blogspot.com/2016/11/define-intronic-exonic-and-intergenic.html it is for hg19, but you can just change to hg38. ...
written 5 weeks ago by tangming2005 • 2.1k
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Answer: A: bulk download in ENCODE
... try ENCODExplorer package if you use R. http://bioconductor.org/packages/release/bioc/html/ENCODExplorer.html ...
written 5 weeks ago by tangming2005 • 2.1k
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Comment: C: ChIP-seq analysis - More peaks in IP samples without activating the TF
... I know for macs1, if you have IP and Input with different amount of reads, it will downsample the higher reads sample to the lower reads sample. if you only have 8M in the untreated cells, the input (15million) will be downsampled to 8 million as well. This might affect your peak calling results. A ...
written 5 weeks ago by tangming2005 • 2.1k
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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 8 weeks 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 8 weeks ago by tangming2005 • 2.1k

Latest awards to tangming2005

Popular Question 24 days ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Good Question 5 weeks ago, asked a question that was upvoted at least 5 times. For what tools to visualize structural variants VCF files?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 9 weeks ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
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
Appreciated 3 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Appreciated 3 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Great Question 4 months ago, created a question with more than 5,000 views. For htseq-count for pair-end RNA-seq
Popular Question 4 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 4 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 4 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Popular Question 5 months ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
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Popular Question 9 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 9 months ago, created a question with more than 1,000 views. For Are adapters removed for fastq files dumped from sra from GEO?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
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Appreciated 11 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Appreciated 11 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 11 months ago, created a question with more than 1,000 views. For RNAseq heatmap.2 log2FC clustering
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