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Recent Replies
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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dsull
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Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
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I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
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Ankit
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what is your txdb?
can you explain your experiment in detail?
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cmdcolin
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paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
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rpolicastro
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Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
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ATpoint
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It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
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ATpoint
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DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
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dsull
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Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question...
In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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RNAseqer
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Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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Nitin Narwade
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Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
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Enrique
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Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
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ATpoint
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No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
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Enrique
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Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
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Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
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