User: henryvuong

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henryvuong770
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Posts by henryvuong

<prev • 22 results • page 1 of 3 • next >
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Comment: C: How Can I Find Out Unknown Illumina Barcode.
... I think you should sort before count uniq, then sort again to see the most frequent at the top of the list. grep ^@HISEQ lane1_Undetermined_L001_R1_001.fastq | cut -d":" -f10 | sort -r | uniq -c | sort -nrk1,1 > barcodes.txt ...
written 4.4 years ago by henryvuong770 • updated 4 months ago by RamRS26k
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Frame number in Oncofuse output
... Hi,  I applied Oncofuse to annotate fusion genes from DNA-seq and would like to determine if the fusion is in-frame or not. Oncofuse provided 5_FRAME (frame of translated 5'FPG), 3_FRAME (frame of translated 3'FPG) and FPG_FRAME_DIFFERENCE (difference in 5' and 3' FPG frames). Their values are 0, 1 ...
fusion oncofuse written 5.4 years ago by henryvuong770 • updated 5.4 years ago by mikhail.shugay3.4k
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Comment: C: cravat.us web services, unable to understand what to do
... First, please check your input file. Here's an example input (cravatinput.txt) #UID / Transcript / AA change / Sample ID (optional) TR1 NM_001126116.1 D127Y TCGA-02-0231 TR2 NM_001144919.1 R162Q TCGA-02-3512 TR3 NM_000321.2 Q702K TCGA-02-3532 TR4 NM_0 ...
written 5.9 years ago by henryvuong770 • updated 18 months ago by RamRS26k
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Comment: C: cravat.us web services, unable to understand what to do
... Thank for the idea. I have to add @ before the input.txt for it to work. Otherwise, it shows errormsg as "there is no input mutation" ...
written 5.9 years ago by henryvuong770 • updated 3 months ago by RamRS26k
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Comment: C: How To Create Mutation Diagram In R Or In Any Tools?
... Please PM me your email.  ...
written 6.0 years ago by henryvuong770
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Answer: A: Problem With Picard Dedup In Illumina Alignment Pipeline
... Hi, I encountered the same error with picard tool version 1.96 while running CollectTargetedPcrMetrics. I tried the same command line with picard version 1.79 then it worked fine. ...
written 6.7 years ago by henryvuong770
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Comment: C: Is There A Way To Do Bulk Data Download From The Cbioportal?
... have you tried cgds (R package) ? http://www.cbioportal.org/public-portal/cgds_r.jsp ...
written 6.7 years ago by henryvuong770
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Answer: A: How Can I Generate A Venn Diagram In R For A Given Csv File
... I like using Venny (http://bioinfogp.cnb.csic.es/tools/venny/) the most. It's very intuitive. I tried it with your example data. ...
written 6.9 years ago by henryvuong770
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Answer: A: Database Of Tumor Suppressors And/Or Oncogenes
... There is a nice table of oncogenes and tumor suppressor genes from this publication (Supplementary material) Vogelstein, B., Papadopoulos, N., Velculescu, V., Zhou, S., Diaz, L. & Kinzler, K. Cancer genome landscapes. Science (New York, N.Y.) 339, 1546–58 (2013). http://www.sciencemag.org/conten ...
written 7.0 years ago by henryvuong770
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Answer: A: Mutect Vcf Output
... the latest version of MuTect (ver 1.1.4) downloaded from (http://www.broadinstitute.org/cancer/cga/mutect_download) can generate vcf output with --vcf parameter. hope it helps ...
written 7.0 years ago by henryvuong770

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Appreciated 4.1 years ago, created a post with more than 5 votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
Epic Question 4.1 years ago, created a question with more than 10,000 views. For How To Create Mutation Diagram In R Or In Any Tools?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Frame number in Oncofuse output
Scholar 4.1 years ago, created an answer that has been accepted. For A: Readvcf In R
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Mutect Vcf Output
Great Question 4.6 years ago, created a question with more than 5,000 views. For How To Create Mutation Diagram In R Or In Any Tools?
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: How Can I Generate A Venn Diagram In R For A Given Csv File
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Popular Question 5.6 years ago, created a question with more than 1,000 views. For 10Kb Reads From Illumina Hiseq
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Database Of Tumor Suppressors And/Or Oncogenes
Good Question 5.8 years ago, asked a question that was upvoted at least 5 times. For How To Create Mutation Diagram In R Or In Any Tools?
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Commentator 6.0 years ago, created a comment with at least 3 up-votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Database Of Tumor Suppressors And/Or Oncogenes
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: How To Visually Display What Protein Domains Are Affected By A Mutation
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Student 6.0 years ago, asked a question with at least 3 up-votes. For How To Create Mutation Diagram In R Or In Any Tools?

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