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User: zhenyisong

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zhenyisong • 120
Reputation:
120
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Trusted
Location:
China
Last seen:
2 months ago
Joined:
5 years, 8 months ago
Email:
z*********@gmail.com

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Posts by zhenyisong

<prev • 28 results • page 1 of 3 • next >
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Answer: A: GATK current version downloading fails
... you can try [miniconda][1] to mange your software version. GATK4 has already lifted its restriction. conda install -c bioconda gatk [1]: https://conda.io/miniconda.html [2]: https://bioconda.github.io/ ...
written 3 months ago by zhenyisong • 120
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Comment: C: What is the best method ChIPseq differential binding analysis?
... Beside @Rory's suggestion, I would suggest you to pay attention to [this paper][1] (The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses) about the wet procedure. Sebastian's work argued that there were few overlaps between different pipelines. [1]: h ...
written 5 months ago by zhenyisong • 120
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Answer: A: indexed human reference genome
... [iGenomes][1]. The ftp site provides the indexed human genomes for different versions. You can also download the corresponding assembly from NCBI or ENSEMBL or UCSC. And create your own indexed genome using bwa index -a bwtsw [1]: https://support.illumina.com/sequencing/sequencing_software ...
written 6 months ago by zhenyisong • 120
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Comment: C: Strand specific pair end Illumina sequencing
... I read the [protocol here][1]. for Ovation RNA-Seq Systems 1–16 for Model Organisms. The figure 1 at PDF page 6 said that this kit uses the first strand to construct the library. (Second Strand Synthesis with Nucleotide Analog, Ligation with Nucleotide Analog-marked Adaptors). But Please contact Nu ...
written 15 months ago by zhenyisong • 120
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Comment: C: Strand specific pair end Illumina sequencing
... I think you used the second strand to construct the library due to to the inference from the output by RSeQC. The second strand here means that the sequence order is in line with the mRNA and not the complementary DNA (cDNA). Sense-strand. If this is the case, you should use the FR. But you should c ...
written 15 months ago by zhenyisong • 120
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zero read_count output from mirDeep2 quantification procedure. How to trouble shoot?
... I installed the mirDeep2. The version is miRDeep2.0.0.8 and last modification time is 21/04/2016. bowtie --version #bowtie version 0.12.9 #64-bit #Built on igm1 #Sun Dec 16 14:36:32 EST 2012 #Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-50) #Options: -O3 -m64 -Wl ...
software error rna-seq mirdeep2 written 20 months ago by zhenyisong • 120
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Comment: C: Gene profiling (RNA-seq or Microarray data) to explore public database to find s
... Thanks. It is just what I mean. ...
written 24 months ago by zhenyisong • 120
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Comment: C: High-throughput sample BLAST
... @b.nota and @Farbod Query input: a list of genes with their expression value. (my study result from microarray or RNA-seq data) Database: archive all high-throughput results (microarray or RNA-seq) from various experiments Output: find the similar experiment in the database. I mean, I want to fi ...
written 2.0 years ago by zhenyisong • 120
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Gene profiling (RNA-seq or Microarray data) to explore public database to find similar samples
... My aim is to use the gene profiling of my sample (RNA-seq or Microarray data) to explore the database to find the similar samples. I used my sample and public data and performed Spearman correlation, but the result has a huge batch effect.Is there any implemented solution to my problems? Thanks. ...
sample correlation microarray rna-seq written 2.0 years ago by zhenyisong • 120 • updated 2.0 years ago by WouterDeCoster ♦ 30k
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Comment: C: Remove Batch Effect From RNAseq with SVAseq and Combat
... @cankutcubuk and @yasinkaymaz Since the data has internally been transformed to log format, does this mean we can not analyze the data using DESeq2 or edgeR or Limma? Limma uses voom to transform the data and has a weight matrix. Other two package require count data. If I want to use these three pac ...
written 2.3 years ago by zhenyisong • 120

Latest awards to zhenyisong

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: indexed human reference genome
Scholar 6 months ago, created an answer that has been accepted. For A: indexed human reference genome
Popular Question 11 months ago, created a question with more than 1,000 views. For Is there any specific quality metrics for lncRNA-seq or miRNA-seq?
Popular Question 11 months ago, created a question with more than 1,000 views. For single cell RNA-seq anlysis, PCA method, how to choose variables which contribute most to components?
Popular Question 11 months ago, created a question with more than 1,000 views. For PWM matching alogrithm
Popular Question 13 months ago, created a question with more than 1,000 views. For Is there any specific quality metrics for lncRNA-seq or miRNA-seq?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For single cell RNA-seq anlysis, PCA method, how to choose variables which contribute most to components?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For single cell RNA-seq anlysis, PCA method, how to choose variables which contribute most to components?
Student 3.4 years ago, asked a question with at least 3 up-votes. For single cell RNA-seq anlysis, PCA method, how to choose variables which contribute most to components?
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