User: Zhenyu Zhang

gravatar for Zhenyu Zhang
Zhenyu Zhang240
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240
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Location:
United States
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1 day, 2 hours ago
Joined:
5 years, 1 month ago
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Posts by Zhenyu Zhang

<prev • 56 results • page 1 of 6 • next >
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Answer: A: Is TCGA PRAD RNA-seq data strand specific?
... The short answer is no. The specific RNA-Seq library preparation kit TCGA used actually "could" support stranded library; however, it was used in a manner that libraries are actually strandless. ...
written 1 day ago by Zhenyu Zhang240
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Comment: C: Why is TCGA Genomic Data Commons missing some data?
... Btw, if you were in the loop during the old TCGA DCC era, there was an emergency redaction of TCGA LAML data for a couple of months. GDC happened to pull TCGA data from DCC and CGHub during that period of time, so that's why they are missing ...
written 6 weeks ago by Zhenyu Zhang240
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Comment: C: TCGA COAD and READ annotations missing from GDC commons?
... Such annotation still exist in GDC as "annotation" nodes in the GDC Database, and queryable using APIs. As all metadata in GDC are maintained in a single Graph Database and accessible by API (and UI), there are no separate "annotation database" or "annotation manager" in GDC. ...
written 6 weeks ago by Zhenyu Zhang240
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Comment: C: How to find On-Target and Off-Targer percentage of reads?
... We used HSmetics too. But some large WXS files have extreme memory requirement. Sometimes we have to double memory allocation from 16G to 32G, or even 64G to get this done. We don't see similar problems with WGSmetrics no matter how big the file is. Does anyone know alternatives of HSmetrics? ...
written 7 months ago by Zhenyu Zhang240
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Answer: A: WGS for TCGA HNSC project
... I don't know why the sequencesource will state otherwise, but if there is sdrf describing this vcf is derived from a WGS CGHub analysis_id/bam file, then it should be WGS. As to MAFs, ppl will not make project-level MAFs out of WGS calls given the file will be 100 times larger. ...
written 17 months ago by Zhenyu Zhang240
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Comment: C: tumor only variant calling tools
... Looks great, I will have a look. The panel of normals are expected to call CNV from target panels or WXS. ...
written 17 months ago by Zhenyu Zhang240
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Comment: C: tumor only variant calling tools
... Actually tumor only sample doesn't mean there is no normals. I may have overstated what FM is doing, but I really mean is that you can take advantages of tumor impurity, and make probability models if a variant is somatic or germline based on copy number variation, subclonality, and allele frequency ...
written 17 months ago by Zhenyu Zhang240
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Comment: C: tumor only variant calling tools
... hmmm. totally do not remember that post one year ago ...
written 17 months ago by Zhenyu Zhang240
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Comment: C: raw count on TCGA/GDC
... For GDC data, using the browser to select HTSeq count data, of your custom cohort, download the manifest, and use gdc-client to get them all. ...
written 17 months ago by Zhenyu Zhang240
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Comment: C: Differences between FPKM and FPKM-UQ files in gene expression analysis
... FPKM and UQ-FPKM are calculated by GDC just for legacy reason, because ppl used to use FPKM data, and UQ provides a method for normalization. However, for any serious analysis, using count data with DESeq/EdgeR are encouraged. ...
written 17 months ago by Zhenyu Zhang240

Latest awards to Zhenyu Zhang

Popular Question 5 months ago, created a question with more than 1,000 views. For Impute2 race specific panel?
Popular Question 14 months ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
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Popular Question 14 months ago, created a question with more than 1,000 views. For tumor only variant calling tools
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Popular Question 14 months ago, created a question with more than 1,000 views. For gene set enrichment / GO
Popular Question 15 months ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 16 months ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
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Popular Question 22 months ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Survival Analysis Using Tcga Data
Popular Question 23 months ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For MACH imputation result QC
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Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Survival Analysis Using Tcga Data
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Survival Analysis Using Tcga Data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For gene set enrichment / GO

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