User: wangdp123

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wangdp12390
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Posts by wangdp123

<prev • 33 results • page 1 of 4 • next >
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How to normalize the bam files for RNA-Seq samples for visualization
... Hi there, I would like to compare the visualizations of bam files from different RNA-Seq samples to get a view of the differences among samples. The software would be golden helix software or IGV viewer. I am wondering if there is a way to normalize the bam files by taking into account the total r ...
normalization rna-seq visualize written 4 hours ago by wangdp12390 • updated 1 hour ago by trausch900
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The inclusion or exclusion of NR transcripts in RefSeq gene annotation in the RNA-Seq analysis
... Hi there, The human Refseq gene annotation includes protein-coding genes and non-coding genes and even for the protein-coding genes it is possible to include mRNA (NM_) and non-coding RNAs (NR_) for the same gene at the same time. For the RNA-Seq analysis, is there a need to remove all the NR_ tra ...
refseq rna-seq written 21 days ago by wangdp12390 • updated 19 days ago by h.mon13k
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The estimate index of codon bias
... Hi there, Could anybody suggest a number of indexes for measuring the codon bias of each gene in a genome without the expression data? I know one of the most famous indexes is CAI (Codon adaptation Index) but this will need a prior knowledge of a group of high-expressed genes. But what if the geno ...
codon bias written 27 days ago by wangdp12390
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Cluster genes based on their codon usage
... Hi there, I wonder if anybody knows how to cluster genes based on their codon usage and identify the various groups of genes that posses different codon usage patterns, which is analogous to the identification of gene family such as orthoMCL approach. I know there is one way to do the heatmap but ...
cluster gene codon usage written 6 weeks ago by wangdp12390
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Process the VCF files for a huge number of samples
... Dear Colleague, I am processing the VCF files from thousands of samples from exome-sequencing. I would like to take the three steps as follows: 1. Identify the homozygous SNPs. 2. Identify the minor allele SNPs. 3. identify the SNP/InDel that have deleterious effects on protein function such as n ...
vcf indel exome-seq snp written 7 weeks ago by wangdp12390
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Tool: GCevobase: an evolution-based database for GC content in eukaryotic genomes
... Hi there, I am happy to introduce a new database that contains the essential genome composition information from 1118 eukaryotic genomes that includes GC content, GC1, GC2, GC3 and GC4d (GC content at four-fold degenerate sites). The relevant reference: GCevobase: an evolution-based database for ...
genome gc content evolution tool written 10 weeks ago by wangdp12390
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How to find the hub genes in the gene co-expression network constructed by WGCNA
... Hi there, I have used WGCNA tool to construct a gene co-expression network and identified several modules. I am keen to discover the hub genes (the gene that has the maximum connections with other genes in a module) in each module. Does anybody know how to pinpoint the hub genes? Via which scripts ...
wgcna hub gene written 12 weeks ago by wangdp12390 • updated 12 weeks ago by Kevin Blighe16k
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... Hi Kevin, Your detailed answer is highly appreciated. I have a further question. In fact, I have about 40000 genes with FPKMs for the network construction, and I try to increase maxBlockSize = 40000, in which way the calculation is running extremely slow. In this case, do you think I need to fil ...
written 5 months ago by wangdp12390
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The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
... Hi there, I am learning to use RNA-Seq data matrix with WGCNA to build up gene-co-expression network. I know WGCNA was designed for the microarray data but after appropriate handling, it is also applicable to the RNA-Seq data. Regarding the format of the input data, I have several concerns: 1. T ...
wgcna network written 5 months ago by wangdp12390 • updated 5 months ago by Kevin Blighe16k
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The strategy to annotate the transcriptional factors from transcripts
... Hi there, I have found that the plantdb database is quite useful in my work. I have tried two different ways to annotate the transcription factors for my transcripts. 1. Blastx my transcript sequences against protein sequences of All TFs in PlantTFDB 4.0. 2. Use the functional module of Transcrip ...
annotation tf written 7 months ago by wangdp12390

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