User: Ginsea Chen

gravatar for Ginsea Chen
Ginsea Chen110
Reputation:
110
Status:
Trusted
Location:
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Last seen:
5 months ago
Joined:
3 years, 7 months ago
Email:
g*********@hotmail.com

Posts by Ginsea Chen

<prev • 83 results • page 1 of 9 • next >
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Answer: A: Access data from very big vcf files in R
... You can extract your target information through following linux shell command: zcat ExAC.r1.sites.vep.vcf.gz | head -n x+ | awk '{print $1 $2}' > target.bed x means the number of the first information line; target.bed is your result file. This is a simple operation, you can contact me (cginsea ...
written 6 months ago by Ginsea Chen110
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How to use molecular docking to verify positive selection site
... Dear all. I used PAML to identify four positive selection site and posted this information to a manuscript. A reviewer suggested that I should use some dry or wet experiment method to verify these sites, such as molecular docking. I have none of the experiences to perform molecular docking analyses ...
molecular docking positive selection site written 6 months ago by Ginsea Chen110 • updated 6 months ago by aka001180
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How to extract primates tree model and placental mammal model from vertebrate model in phyloP46way
... Dear All. In the method part of phyloP46way (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way), they said that they extract primates tree model and placental mammal model from the vertebrate model, while this description has no detail methods introduction, such as software or optio ...
phylop46way written 7 months ago by Ginsea Chen110 • updated 6 months ago by Biostar ♦♦ 20
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Repeat Position in TGP phase3 database vcf file
... Dear All. I am a user of 1000 genomes database, I have downloaded vcf file from UCSC (http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/). In Chromosome X(ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz), I found some repeat position, just like follows: 26 ...
vcf 1000 genomes tgp phase3 written 9 months ago by Ginsea Chen110
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How to get rapidly evolution go categories through binomial probability
... Dear all. In paper which named as "**Initial sequence of the chimpanzee genome and comparison with the human genome", published on nature (Vol 437|1 September 2005|doi:10.1038/nature04072)**, the author described a new method about how to get rapidly evolution go categories, the correspondent inform ...
binomial probability annotation go evolution; written 13 months ago by Ginsea Chen110 • updated 5 months ago by Biostar ♦♦ 20
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How to transfer non numeric enrichment factor to numeric in RDA analysis
... Dear all I tried to use vegan of R to perform RDA analysis for 16s rDNA datasets, while my enrichment factor is not numeric, such as one group data from Young species, while another group from old species. So, **my question is how to transfer this non numeric enrichment factor to numeric(like PH val ...
enrichment factor 16srdna rda written 15 months ago by Ginsea Chen110
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Inconsistent among simpson index curve and shannon index curve in alpha diversity analysis using QIIME
... Dear all ---------- I have used qiime to pick OTUs from 16s DNA datasets with 5 samples. Singletons OTUs have been filtered with -n 2 option in filter_otu_from_otu_table.py script. Then, I want to perform alpha diversity analysis by choosing observed-species, chao1, shannon, and simpson index. ---- ...
shannon index simpson index alpha diversity qiime written 15 months ago by Ginsea Chen110 • updated 15 months ago by Vijay Lakhujani1.7k
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Error about pbtranscript-tofu installation
... Dear all! I tried to install pbtranscript-tofu as follows:https://github.com/PacificBiosciences/cDNA_primer/wiki/Setting-up-virtualenv-and-installing-pbtranscript-tofu While a error message reported in the "make" step, ``` git clone git://github.com/PacificBiosciences/cDNA_primer.git cd cDNA_prime ...
installation python pacbio pbtranscript-tofu written 21 months ago by Ginsea Chen110 • updated 21 months ago by Ram13k
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Answer: A: NCBI-SRA File Downloader
... wget is so slow, you can download it by using aspera software. The more detail information about this method was pasted in my blog: http://blog.sciencenet.cn/blog-1334016-923025.html. ...
written 23 months ago by Ginsea Chen110
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How to get the sources of genes in genome annotation
... Dear all! I used evidencemodeler (EVM) to improve the annotation of a plant genome drived from multiple sources (i.e. RNA-seq, de novo prediction, peptide sequences of related species), and now I want to know how get how many genes origined from a special source, such as how many genes were based on ...
genome annotation written 23 months ago by Ginsea Chen110

Latest awards to Ginsea Chen

Great Question 13 months ago, created a question with more than 5,000 views. For Errors about ggplot2 packages of R language install in Ubuntu server
Popular Question 13 months ago, created a question with more than 1,000 views. For Some problems about NCBI data downloading using Aspera
Popular Question 13 months ago, created a question with more than 1,000 views. For About gene expression heatmap
Popular Question 18 months ago, created a question with more than 1,000 views. For About gene expression heatmap
Popular Question 19 months ago, created a question with more than 1,000 views. For About gene expression heatmap
Popular Question 20 months ago, created a question with more than 1,000 views. For About gene expression heatmap
Popular Question 21 months ago, created a question with more than 1,000 views. For Some problems about NCBI data downloading using Aspera
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Some problems about cummeRbund running
Popular Question 2.1 years ago, created a question with more than 1,000 views. For About gene expression heatmap
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For About expressionBarplot () in cummeRbund
Popular Question 2.3 years ago, created a question with more than 1,000 views. For There were no GEOquery function after installing
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Errors about ggplot2 packages of R language install in Ubuntu server
Popular Question 2.5 years ago, created a question with more than 1,000 views. For There were no GEOquery function after installing
Great Question 3.0 years ago, created a question with more than 5,000 views. For Errors about ggplot2 packages of R language install in Ubuntu server
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Errors about ggplot2 packages of R language install in Ubuntu server
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to calculate FPKM values of interested gene
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Errors about ggplot2 packages of R language install in Ubuntu server

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