User: wangdp123
wangdp123 • 60
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Posts by wangdp123
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... Hi, thanks for this. I have looked through the log2, rlog and VST normalization methods mentioned in this workflow. But my data are from different species, so in this case, I believe that some calculations should be made to normalize the gene lengths. Any thought about this?
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written 8 weeks ago by
wangdp123 • 60
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... Hi there,
I am trying to use RNA-Seq data from a large number of samples to draw the phylogenetic tree based on FPKM values in order to show the relationship among all samples. (The samples include various species, tissues and treatments.)
Are there any elegant tools implemented for this purpose?
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... Hi there,
I am trying to understand how to define "between_species_paralog" in Ensembl and EnsemblGenomes and found out the definitions here:
For Ensembl: (http://www.ensembl.org/info/genome/compara/homology_method.html)
> Currently, we only annotate between_species_paralog when there is no
&g ...
written 9 weeks ago by
wangdp123 • 60
• updated
9 weeks ago by
Emily_Ensembl ♦ 13k
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... Hi there,
I am trying to use TopGO to perform some GSEA analyses (Gene Set Enrichment Analysis). In order to do this, I have done the differential expression analysis for all genes and produced the P-values and Fold change values for each gene.
I am aware of the fact that TopGO needs a ranked gene ...
written 11 weeks ago by
wangdp123 • 60
• updated
11 weeks ago by
kennethcondon2007 • 810
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... Hi there,
I am working on the annotation of genes assembled from RNA-Seq data from a non-model species and I have tried to use interproscan to get the GO terms based on the protein sequences predicted by Transdecoder. It seems that only a limited number of genes have predicted ORF and only a propor ...
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... Hi, it is not a model organism.
I have annotated the GO terms for each gene in this species.
What I need to do is to input my GO assignment rather than use the public annotated one to do enrichment analysis with my identified up-regulated or down-regulated gene lists.
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written 3 months ago by
wangdp123 • 60
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5 follow
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... Hi there,
I have assigned all GO terms to each gene in my study through interproscan, and I am going to do some GO enrichment analysis based on my DEGs and my GO annotation database.
Could anybody suggest some decent software for this purpose?
Many thanks,
Tom
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... Hi, here is another option for genome alignment in a unit of genes.
Good to try:
http://ec2-52-40-200-174.us-west-2.compute.amazonaws.com/LCGserver/
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written 4 months ago by
wangdp123 • 60
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... Hi,
Thank you for the explanation.
Any clue to understand the tables in Compara.88.protein_default.nh.emf.gz and Compara.88.protein_default.nhx.emf.gz and parse them if I try to identify the one-to-one, one-to-many and many-to-many relations?
Cheers,
Tom
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written 4 months ago by
wangdp123 • 60
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... Hi there,
I am trying to retrieve all the orthologs and paralogs for all fungi species in ensembl fungi database, but I couldn't find a way to download them in bulk. I know Biomart provides the service for manual collection but it doesn't work for my purpose.
For example, I would like to download ...
written 4 months ago by
wangdp123 • 60
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