User: hwu12
hwu12 • 50
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Posts by hwu12
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... Thanks :-) It is just a little sad that the homologs are based on TAIR10 and an older version of Tomato transcriptome. I guess If I want to use the latest version of tomato annotation and Araport 11 annotation, I will have to blast them myself. ...
written 10 days ago by
hwu12 • 50
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... It seems to me that the orthoDB is for checking few genes. Can we use it to generate a list of all homolog pairs between two species? Thanks! ...
written 11 days ago by
hwu12 • 50
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... I was wondering if there is a database for the homologs between two plants. Specifically, I am looking for a list of homologs between tomato and Arabidopsis. Thanks! ...
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... Thanks so much, James!
For others interested in this method, a user's guide can be found at
https://github.com/stephaniehicks/qsmooth/blob/master/vignettes/qsmooth-vignette.pdf ...
written 11 days ago by
hwu12 • 50
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... It is a very good idea to prioritizing genes instead of normalizing genes. Thanks, Michele. ...
written 11 days ago by
hwu12 • 50
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... I know people use a selected set of housekeeping genes as controls for qPCR analysis. Could we do that in RNA-Seq analysis? Could you provide a reference for that? Thanks! ...
written 14 days ago by
hwu12 • 50
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... Thanks, h.mon! This link you suggested does provide a nice example. ...
written 14 days ago by
hwu12 • 50
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... Please correct me if I am wrong. I guess it is difficult to get "normalized counts" for very different samples. Indeed, most people just go head use these tools with different organs or tissues, but I just wonder if there is a better way. :-)
Another way to think about this, maybe it is meaningless ...
written 14 days ago by
hwu12 • 50
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... e.g. For example: "Still, it is important to keep in mind that even these methods are based on an assumption that most genes are equivalently expressed in the samples." from https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-91 ...
written 14 days ago by
hwu12 • 50
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... Standard tools for differential expression analysis tools (e.g. edgeR and DESeq2) assume that most genes in the samples are equally expressed, and only a small fraction of genes are differentially expressed. I was wondering how we can compare two very different RNA samples. For example, one from mus ...
written 14 days ago by
hwu12 • 50
• updated
12 days ago by
James Ashmore • 1.7k
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