User: nancydong20

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nancydong2060
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Posts by nancydong20

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Comment: C: WGCNA analysis for normalised data expression data sets
... Well, trait data can be added in later if you find a particular module of interest and think that it could be correlated with a trait that you are seeing (just my random guess, like if you are seeing variations in how well each sample is "developing"). Integrating trait data basically allows you to ...
written 5 weeks ago by nancydong2060
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Comment: C: HISAT2 software installation
... Yes, conda works with Linux. You can think of it as kinda like perlbrew for python. But it really doesn't seem like an installation issue if your original .`/hista2` command worked. You can download and install Miniconda on Linux from here: https://conda.io/miniconda.html After installing Minicon ...
written 5 weeks ago by nancydong2060
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Answer: A: HISAT2 software installation
... First, this doesn't seem to be an installation issue. You can try installing hisat2 using conda, which will give a more hassle-free installation. Is the hisat2 folder in your PATH? If not, then just typing `hisat2 -h` would likely give you "command not found". I see in your first post that you used ...
written 5 weeks ago by nancydong2060
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Bayesian network analysis of RNA-seq data to infer upstream/downstream genes
... Hello! I am currently using RNA-seq to examine the roles of a few key proteins in the transcriptional response underlying a certain condition. I came across this interesting [article][1] where Bayesian Network Analysis (using the R package *deal*) was used to analyze RNA-seq data to infer which ge ...
bayesian network analysis rna-seq written 5 weeks ago by nancydong2060
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Comment: C: Examining connectivity of specific genes in WGCNA
... Fantastic, I will go look at that. Thank you very much! ...
written 6 weeks ago by nancydong2060
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Comment: C: Examining connectivity of specific genes in WGCNA
... Thank you very much for the suggestions! Regarding your suggestion #3, if I have three experimental groups such as control, "stimulated" and knockdown+"stimulated", do I need 35 samples per group? As a side question, is WGCNA a suitable approach if I this is what I'm planning: 1. First characte ...
written 6 weeks ago by nancydong2060
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Comment: C: Examining connectivity of specific genes in WGCNA
... Thank you very much! ...
written 6 weeks ago by nancydong2060
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Examining connectivity of specific genes in WGCNA
... Hello! I am currently learning about WGCNA as preparation for an up-coming project, studying a potential novel transcription factor. I am interested in seeing which genes are expressed in a correlated manner with my transcription factor, can WGCNA be used for this? Thank you very much for shedding ...
wgcna written 6 weeks ago by nancydong2060 • updated 6 weeks ago by ildem20
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RepeatModeler and RepeatMasker for non-model species
... Hello everyone! I am trying to analyze repeat elements in a new draft genome of a non-model organism. I used RepeatModeler to build a *de novo* repeat library, and then used RepeatMasker (rmblastn version 2.2.27+) to mask the genome. In the .tbl output, I see that no simple repeats or low complexi ...
repeatmasker repeatmodeler written 9 weeks ago by nancydong2060
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Comment: C: A question about Perl symbol lookup error
... Okay sure, thank you very much for letting me know! ...
written 9 weeks ago by nancydong2060

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