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Recent Replies
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
GenoMax
152k
What is the main aim here? To recover reads that are NOT host.
Using some % cutoff is not a great strategy and reads will map by chance be…
Comment: GSEA analysis
by
Ahmed
•
0
I believe you are right. My mistake! I am confusing NES with upregulation/downregulation, I think. It is a little confusing.
Comment: how to make a circular plot of variants
by
Pierre Lindenbaum
166k
https://circos.ca/tutorials/lessons/
Comment: GSEA analysis
by
nux
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50
try log2FoldChange * -10logpvalue and if possible can you cross check it with the library in the link I sent earlier. How can you tell that…
Comment: GSEA analysis
by
Ahmed
•
0
I used featureCounts to get gene-level counts from RNA-seq BAMs, then ran DESeq2 to get log2FoldChanges and adjusted p-values. Then I took …
Comment: GSEA analysis
by
nux
▴
50
no, walk me through your process and let's check how did you end up with different regulation. For visualization, you can check some ideas …
Answer: GSEA analysis
by
nux
▴
50
Ca you elaborate the steps that you did for your analysis. For all just to make sense or to establish the context of your analysis, make su…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
What are your thoughts of first Mapping my target reads at say 95% or higher first, then doing host removal of the remaining reads, and the…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
Yes, I have read about that tool, as it appeared to be what I was looking for. I tried installing the BBMap on my Windows computer, but c…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
GenoMax
152k
> I can only work with the tools available on Galaxy.org
That requirement is likely going to make this very difficult to accomplish, ther…
Answer: Why little difference in RNAseq alignment when flipping forward and reverse stra
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swbarnes2
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Bowtie doesn't know what read should go in what direction. It's aligning to genome, it will just flip things to make the alignment work.
…
Answer: DESeq2 design for differential expression with 2 timepoints and 2 controls
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swbarnes2
15k
Adding interactions is not correct for most of what you are doing. Time + treatment is what you want for 1 and 2. For questions like 3, m…
Comment: Venn Diagram
by
WouterDeCoster
48k
I don't think that is possible. You may have some luck if you look for an Euler diagram instead. But as @lievensterck said, it is just not …
Comment: Venn Diagram
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lieven.sterck
15k
I don't think there exist any software that will generate this.
Personally I would not go above 5-6 , as those higher numbers become reall…
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