User: Liye Zhang

gravatar for Liye Zhang
Liye Zhang80
Reputation:
80
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Trusted
Location:
United States
Last seen:
1 year, 3 months ago
Joined:
6 years, 9 months ago
Email:
b***********@gmail.com

Posts by Liye Zhang

<prev • 14 results • page 1 of 2 • next >
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Job: A Computational Biology/Bioinformatics Postdoctoral Fellow position in Shanghai Tech University, Shanghai, China
... **Job Description** Applications are invited for a Postdoctoral Fellow position in the lab of Dr Liye Zhang at School of Life Science and Technology of Shanghai Tech University, Shanghai, China. We are seeking a highly-motivated applicant interested in the using computational approaching to advan ...
biostatistics next-gen dna-seq job rna-seq written 16 months ago by Liye Zhang80
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Comment: C: Input Error Using Varscan2.3
... Hi, I wonder if you have solved the problem, if so, would you mind giving me some suggestions on how to solve this? ...
written 4.4 years ago by Liye Zhang80
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Comment: C: Input Error Using Varscan2.3
... I resolved the problem, but this is something you might want to know. I tried the samtools mpileup and pipe to Varscan. It did not work when I used samtools 0.1.19 for Varscan2.2.11 ,Varscan2.3.5 and Varscan2.3.6. But if I use the samtools 0.1.18, all versions worked. conclusion: the newer version ...
written 4.4 years ago by Liye Zhang80
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Comment: C: How To Set The Proper Parameters When Using Hotnet Web Server?
... Thanks for yout help and comments. Yes, I have looked carefully through the example files and README you pointed out before I post the questions. However, I am still not clear about the parameters I mentioned before. In fact, the some file format requirement(copy number alteration ones) for the loca ...
written 5.5 years ago by Liye Zhang80
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Comment: C: How To Set The Proper Parameters When Using Hotnet Web Server?
... I definitely agree with you, I sent them email twice, still no response yet... That is why I am trying to get help from the community. ...
written 5.5 years ago by Liye Zhang80
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How To Set The Proper Parameters When Using Hotnet Web Server?
... Hi, I wonder whether anyone has experience with HotNet, http://ccmbweb.ccv.brown.edu/hotnet/ I tried to use its online (web) version, but I have several questions regarding to the input for the program, can someone help me with it? Thanks a lot. I want to ask few simple questions about running Hotn ...
network interaction web written 5.5 years ago by Liye Zhang80 • updated 5.5 years ago by Chris Miller20k
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Answer: A: Why Do Genome Features With Identical Coordinates Show Different Fpkm Values? (T
... I check the annotation for DDX11L1 of chr1, which spans 11869 to 13670. And RP11-34P13.3 spans 29554 to 30039. And Has-mir-1302-2 starts from 30366 to 30503. Therefore, I think the locus represents a transcript contig defined by cufflinks, which may include multiple transcripts. And each can have ...
written 5.8 years ago by Liye Zhang80
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(Closed) Why Do Genome Features With Identical Coordinates Show Different Fpkm Values? (Tophat/Cufflinks)
... Hi, all: when I checked my paired-end RNAseq data, I saw some weird result. Figure is here basically two genome features have same coordinate(as highlighted in red), however, their fpkm value is different. I wonder anyone have some ideas why this occur? By the way, I am using Tophat v2.0.4, Cuffl ...
fpkm rna-seq written 5.8 years ago by Liye Zhang80
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Answer: A: Problem With Data Containing Non-Finite Values In Cummerund Processing
... Hi, I got an answer from Seqanswers forum. Just quote it in here, in case you are interested. from "Blanco" " I believe this is caused by fpkm values of zero. When the program takes the log of zero it becomes minus infinite (-Inf) and these values are excluded from the analysis. I think there is a ...
written 5.8 years ago by Liye Zhang80
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(Closed) Problem With Data Containing Non-Finite Values In Cummerund Processing
... Hi,all: Recently, I am trying to identify the differentially expressed genes between two conditions. Each condition has three replicates(paired end). I got a problem when I am trying to analyze the data using Tophat v2.0.4, Cufflinks v2.0.2 and cummeRbund v2.0.0. The problem is that when I try to ...
cufflinks rna-seq written 5.8 years ago by Liye Zhang80

Latest awards to Liye Zhang

Great Question 2.0 years ago, created a question with more than 5,000 views. For Problem With Data Containing Non-Finite Values In Cummerund Processing
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How To Set The Proper Parameters When Using Hotnet Web Server?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Problem With Data Containing Non-Finite Values In Cummerund Processing
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Ask About The Empirical Quality Score Mentioned In Gatk Recalibration Step
Commentator 6.0 years ago, created a comment with at least 3 up-votes. For C: Work With Dnacopy (Bioconductor) And Varscan Copynumber Results

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