Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: zhenyisong

gravatar for zhenyisong
zhenyisong • 120
Reputation:
120
Status:
Trusted
Location:
China
Last seen:
3 days, 1 hour ago
Joined:
5 years, 5 months ago
Email:
z*********@gmail.com

about me

Posts by zhenyisong

<prev • 28 results • page 1 of 3 • next >
0
votes
1
answer
68
views
1
answers
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 5 days ago by zhenyisong • 120
0
votes
1
answer
356
views
1
answers
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 10 weeks ago by zhenyisong • 120
4
votes
1
answer
276
views
1
answers
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 3 months ago by zhenyisong • 120
0
votes
1
answer
829
views
1
answers
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 12 months ago by zhenyisong • 120
0
votes
1
answer
829
views
1
answers
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 12 months ago by zhenyisong • 120
0
votes
0
answers
525
views
0
answers
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 17 months ago by zhenyisong • 120
0
votes
0
answers
623
views
0
answers
Comment: C: Gene profiling (RNA-seq or Microarray data) to explore public database to find s
... Thanks. It is just what I mean. ...
written 21 months ago by zhenyisong • 120
0
votes
0
answers
623
views
0
answers
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 21 months ago by zhenyisong • 120
2
votes
0
answers
623
views
0
answers
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 21 months ago by zhenyisong • 120 • updated 21 months ago by WouterDeCoster ♦ 27k
0
votes
2
answers
11k
views
2
answers
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 2.0 years ago by zhenyisong • 120

Latest awards to zhenyisong

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: indexed human reference genome
Scholar 3 months ago, created an answer that has been accepted. For A: indexed human reference genome
Popular Question 8 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 8 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 8 months ago, created a question with more than 1,000 views. For PWM matching alogrithm
Popular Question 10 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 2.3 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 2.6 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?
Student 3.2 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?
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 667 users visited in the last hour