User: Friederike

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Friederike2.3k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

<prev • 269 results • page 1 of 27 • next >
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Comment: C: Bedtools intersect alternatives available
... is there a difference in how bedtools and bedops interpret the intervals? (i.e., zero-based half open vs. 1-based etc.) ...
written 3 days ago by Friederike2.3k
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Comment: C: Plot of 2 replicates
... Can you share the code (including the `gather` command) and plot that you generated and that you want to optimize? ...
written 4 days ago by Friederike2.3k
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Comment: C: Bedtools intersect alternatives available
... If this is whole-genome sequencing, I recommend first running a basic intersect (either with bedtools or bedops) with just the gene regions, keeping only those bases that overlap with genes for the more detailed annotation tasks looking at exons, introns, etc. Odds are you want to separate the base ...
written 4 days ago by Friederike2.3k
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Answer: A: How is it possible to have more than 25000 genes in counts file?
... >How is it possible to have more than 25000 genes in counts file. If your annotation file (most likely a GTF file?) that you used for generating the counts contained more than 25K gene IDs. For more details than you might ever want to know about annotation caveats, I recommend reading ["A compr ...
written 4 days ago by Friederike2.3k
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... What was the response at the bioconductor support page? What happens when you use "group_treat1_vs_control" as the contrast name for retrieving the results? ...
written 4 days ago by Friederike2.3k
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... Did you check whether those 2% fall into the category of 'lowly expressed'? I think, having the counts in treatment 2 in there plays a role (just look at the `baseMean` values). I'm not super familiar with the nitty-gritty details of how DESeq uses the `contrast` argument for the logFC generation, ...
written 5 days ago by Friederike2.3k
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... what do the rlog- or vst-transformed values look like? gene 7 looks fine to me: ``` gene7 1170 1703 1749 337 339 424 ``` EDIT: I agree, your table contains a couple of puzzling results. Here's a couple of thoughts: * lowly expressed genes tend to show sometimes non-intuitive behaviors due ...
written 8 days ago by Friederike2.3k
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... in your snapshot above, which logFC values seem odd to you? ...
written 9 days ago by Friederike2.3k
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Comment: C: Plot line graph when counts are not automatically given
... are you sure that the entries of `my_data$Coverage` are numbers? what does `str(my_data)` return? ...
written 9 days ago by Friederike2.3k
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... The object generated by `results()` should spell out pretty clearly which comparison you did as in the following example: ``` >DESeq.ds <- DESeq(DESeq.ds) >DGE.results <- results(DESeq.ds) > head(DGE.results) log2 fold change (MLE): condition WT vs SNF2 ## this indicates that the lo ...
written 9 days ago by Friederike2.3k

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Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
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Scholar 5 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells

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