User: tangming2005

gravatar for tangming2005
tangming20052.2k
Reputation:
2,230
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Location:
Houston/MD Anderson Cancer Center
Website:
http://crazyhottommy.b...
Twitter:
@tangming2005
Last seen:
3 days, 6 hours ago
Joined:
4 years, 7 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 • 291 results • page 1 of 30 • next >
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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 9 weeks ago by tangming20052.2k
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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 9 weeks ago by tangming20052.2k
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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 9 weeks ago by tangming20052.2k
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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 4 months ago by tangming20052.2k
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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 4 months ago by tangming20052.2k
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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 4 months ago by tangming20052.2k
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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 4 months ago by tangming20052.2k
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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 4 months ago by tangming20052.2k
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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 months ago by tangming20052.2k
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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 months ago by tangming20052.2k

Latest awards to tangming2005

Student 7 weeks 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 weeks ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Appreciated 3 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Popular Question 3 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 3 months ago, created a question with more than 1,000 views. For convert SNP calls to amino acid change
Popular Question 3 months ago, created a question with more than 1,000 views. For any tutorials for structural variants filtering and prioritization
Popular Question 3 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 4 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For what tools to visualize structural variants VCF files?
Popular Question 5 months ago, created a question with more than 1,000 views. For Get all the translation start site for human genome
Popular Question 6 months ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Appreciated 7 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Appreciated 7 months ago, created a post with more than 5 votes. For A: Peak callers for ChIP seq comparison
Great Question 8 months ago, created a question with more than 5,000 views. For htseq-count for pair-end RNA-seq
Popular Question 8 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 8 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 8 months ago, created an answer that was upvoted at least 5 times. For A: Peak callers for ChIP seq comparison
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Identification of functionally relevant regions from ChIP-seq experiments
Popular Question 9 months ago, created a question with more than 1,000 views. For ChIP-seq analysis tutorial
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