User: zhenyisong

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zhenyisong120
Reputation:
120
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China
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1 week, 6 days ago
Joined:
5 years, 2 months ago
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z*********@gmail.com

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Posts by zhenyisong

<prev • 26 results • page 1 of 3 • next >
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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 14 days ago by zhenyisong120
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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 9 months ago by zhenyisong120
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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 9 months ago by zhenyisong120
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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 14 months ago by zhenyisong120
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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 18 months ago by zhenyisong120
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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 18 months ago by zhenyisong120
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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 18 months ago by zhenyisong120 • updated 18 months ago by WouterDeCoster25k
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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 21 months ago by zhenyisong120
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Comment: C: single cell RNA-seq anlysis, PCA method, how to choose variables which contribut
... I remember that each Principle Component(PC) has its weight. Should we times each weight and compare those four components before selecting the max one? ...
written 2.9 years ago by zhenyisong120
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Comment: C: single cell RNA-seq anlysis, PCA method, how to choose variables which contribut
... I greatly appreciate your help. Thanks again. However, I am wondering if this approach (Option 2) is empirical method or has some convincing reason to do so (reference?)? ...
written 2.9 years ago by zhenyisong120

Latest awards to zhenyisong

Teacher 14 days ago, created an answer with at least 3 up-votes. For A: indexed human reference genome
Scholar 14 days ago, created an answer that has been accepted. For A: indexed human reference genome
Popular Question 5 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 5 months ago, created a question with more than 1,000 views. For PWM matching alogrithm
Popular Question 7 months ago, created a question with more than 1,000 views. For Is there any specific quality metrics for lncRNA-seq or miRNA-seq?

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