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Tommy Tang
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install VEP for annotating variants
VEP is one of the most commonly used variants annotation tools along with annovar , snpEff, but the installation and config can be very intimidating. I just went through an installation process, and put down a gist:

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bwa aln or bwa mem for short reads (36bp)
My ChIP-seq data are 36bp single end reads. I usually use bowtie1 for mapping ChIP-seq reads, but bowtie1 does not handle indels. Since I want to call mutations on the ChIP-seq reads, I have to use another aligner BWA , the most popular mapper written by He...

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Weather and crimes in Chicago
Weather and crimes in Chicago Ming Tang June 4, 2017 How the story starts I was attending 2017 American Society of Clinical Oncology (ASCO) annual meeting in Chicago. It was my first time to do a uber from the airport to our hotel. We had a nice uber driver...

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when NAs are not NAs
Downloading data Using TCGAbiolinks, I downloaded RNAseq data for  LUAD  and  LUSC library ( TCGAbiolinks ) library ( SummarizedExperiment ) # query_rna_LUAD.hg38 <- GDCquery(project = "TCGA-LUAD", data.category = "Transcriptome Profiling", # ...

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SHERLOCK to detect early circulating tumor DNA
Early detection of circulating tumor DNA is quite challenging. Read this comment in Cell : Next-Generation Sequencing of Circulating Tumor DNA for Early Cancer Detection And here comes SHERLOCK( Specific High Sensitivity Enzymatic Reporter UnLOCKing) ! from...

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several very interesting histone modification (epigenetics) papers
If you have read my previous post Misconcept of epigenetics , you will know that: histone modification is not epigenetics! However, recently, three papers in Science actually showed that histone modifications actually have a component of inheritance: Causal...

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sshfs on ubuntu and ssh key
Two things I want to keep a note here: First, if you ever have set up a shh key for connecting to remote server, you need to be aware that password-less shh key only works when your home directory on the server is not 777 (writable by others). see this stac...

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use bash associate array to generate commands
The problem I am running  pyclone  recently to determine the clonality of our collected tumor samples. It needs tumor purity (estimated from sequenza) for input. I have 24 samples, and I want to generate pyclone commands for all of them. The solution I usua...

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How to enable the scroll mode for tmux
tmux config file you can copy  https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources/blob/master/scripts/.tmux.conf  to your home directory. it changed the key binding from  control + b  to  control + a  if you are familiar with...

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How to make a heatmap using character matrix
character matrix to heatmap People are willing to read colors. I will show you how to repesent characters in heatmap.  ComplexHeatmap  can directly translate a dataframe (character matrix) into heatmap. It is good to learn basics of  grid  package which  Co...
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