User: Ginsea Chen

gravatar for Ginsea Chen
Ginsea Chen120
Reputation:
120
Status:
Trusted
Location:
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Last seen:
2 months, 1 week ago
Joined:
4 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 18 months ago by Ginsea Chen120
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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 18 months ago by Ginsea Chen120 • updated 18 months ago by aka001190
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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 19 months ago by Ginsea Chen120 • updated 18 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 21 months ago by Ginsea Chen120
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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 2.1 years ago by Ginsea Chen120 • updated 17 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 2.2 years ago by Ginsea Chen120
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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 2.3 years ago by Ginsea Chen120 • updated 2.3 years ago by biokoala3.6k
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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 2.8 years ago by Ginsea Chen120 • updated 2.8 years ago by RamRS20k
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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 2.9 years ago by Ginsea Chen120
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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 2.9 years ago by Ginsea Chen120

Latest awards to Ginsea Chen

Popular Question 17 months ago, created a question with more than 1,000 views. For Some problems about CODEML
Popular Question 17 months ago, created a question with more than 1,000 views. For Low DE gene numbers after Trinity analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For Javascript-enable bowser for Pfam database
Popular Question 17 months ago, created a question with more than 1,000 views. For Some problems about NCBI data downloading using Aspera
Popular Question 17 months ago, created a question with more than 1,000 views. For Difference of parallel Mrbayes results between SUSE and Ubuntu
Popular Question 17 months ago, created a question with more than 1,000 views. For Something about Microarray-based expression analysis of specifical genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Some problems by using Mrbayes with MPICH2
Popular Question 17 months ago, created a question with more than 1,000 views. For How to define RNA-seq protocol based on NCBI description
Popular Question 17 months ago, created a question with more than 1,000 views. For About gene expression heatmap
Popular Question 17 months ago, created a question with more than 1,000 views. For How to remove transcripts that have poor alignment scores in exonerate analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For Script convert ltr_finder output file to fasta format
Popular Question 17 months ago, created a question with more than 1,000 views. For How to bind MPI parallel processes to specific cores
Popular Question 17 months ago, created a question with more than 1,000 views. For Whether FPKM values can be used to indicate the expression level of genes
Popular Question 17 months ago, created a question with more than 1,000 views. For How to download human whole genome database?
Popular Question 17 months ago, created a question with more than 1,000 views. For Mapping 454 reads to reference genome
Popular Question 17 months ago, created a question with more than 1,000 views. For num_threads option of blast+ was unusable after rmblastn installation
Great Question 2.1 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 2.1 years 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 About gene expression heatmap
Popular Question 2.5 years ago, created a question with more than 1,000 views. For About gene expression heatmap

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