User: MaxF

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MaxF70
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Posts by MaxF

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Comment: C: DESeq2 design with three treatments and the genes common to all
... Thanks Kevin, I ended up doing pariwise comparisons but put the mocks together as one group. Since these cytokine treatments were done at different times, I also included a "batch" condition. Maybe I'm just confused, but I thought this: results(dds, contrast = list(c('condition_treated_vs_unt ...
written 4 weeks ago by MaxF70
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Comment: C: How to make bed file of TSS (approximately 2kb, 1 kb upstream and 1kb downstream
... You lost code formatting for the last few lines. Try writing out your code in a text editor, pasting it into the text box, highlighting the whole thing and then pushing the "code" button in the formatting bar (looks like 1010101). For your specific question, you just need to make a variable that c ...
written 5 weeks ago by MaxF70
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Comment: C: how to find gene ontology for genes using RNA-seq data
... If you want to do this for a lot of genes your best bet is to learn how to use one of the R packages that interacts with a GO database. I haven't used [this one][1], but it looks promising. If you don't know anything about R, it's not that difficult. Download R and R studio, then start out learni ...
written 5 weeks ago by MaxF70
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Comment: C: how to find gene ontology for genes using RNA-seq data
... You would not expect the total number of genes in each category to equal the total number of genes input. This is because genes can map to multiple GO terms (GO terms are highly redundant). You can explore all of the parent-child terms related to a GO term of interest at http://amigo.geneontology.or ...
written 5 weeks ago by MaxF70
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Comment: C: how to find gene ontology for genes using RNA-seq data
... You want the "Statistical overrepresentation test". The option you picked breaks down the gene list to show you the GO terms that are represented in the list, but doesn't tell you which ones are enriched/overrepresented. ...
written 5 weeks ago by MaxF70
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Comment: C: How to make bed file of TSS (approximately 2kb, 1 kb upstream and 1kb downstream
... I'm not sure if you were trying to format your lines in some specific way, but the website didn't insert any line breaks so it's hard to understand. I know how to make a bedfile like you're describing using python, but I don't know Perl very well. Both python and perl have bio-libraries that will ...
written 5 weeks ago by MaxF70
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Comment: C: how to find gene ontology for genes using RNA-seq data
... There's a box on the homepage where you enter IDs (usually 1 per line). Your best best is something like ENSEMBL or Entrez IDs, but it will accept gene symbols/names as well (but they might map to something you don't expect, so be careful). Let's say your list is 100 genes. The site will then find ...
written 5 weeks ago by MaxF70
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Comment: C: padj in DEseq2
... http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#p-values-and-adjusted-p-values Note that the results function automatically performs independent filtering based on the mean of normalized counts for each gene, optimizing the number of genes which will have an adjust ...
written 5 weeks ago by MaxF70
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Comment: C: Use padj instead of p-value to ploting DE genes using EnhancedVolcano
... Hi Kevin, The enhancedVolcano package is awesome, thanks for making it. Is there a reason you use unadjusted pvalue in the vignette? I am working with some data and was trying to weigh the pros and cons of visualizing with adjusted vs unadjusted p values. ...
written 5 weeks ago by MaxF70
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Comment: C: How to make bed file of TSS (approximately 2kb, 1 kb upstream and 1kb downstream
... Can you give a bit more info as to your final goal here? This will help us to help you more effectively. Also, when you say you want the "whole gene" do you mean the boundaries of the whole gene region on the chromosome (including introns, alternative transcripts, UTRs)? This is going to be tens ...
written 5 weeks ago by MaxF70

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Supporter 5 weeks ago, voted at least 25 times.
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Salmon Counts differ in Alignment and Quasi-Mapping mode

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