Moderator: seidel

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seidel6.3k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Answer: A: Gene expression comparison of Cancer and Normal tissue
... Most RNA Seq normalization methods assume that most genes are unchanged between conditions, and should have roughly equal expression (see [Robinson and Oshlack, 2010][1] for example). The data is accordingly adjusted such that the bulk of genes in the middle of the expression range have the same mea ...
written 7 days ago by seidel6.3k
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Answer: A: Single-cell RNA seq
... Yes, you would use the hg19 fat sequence and gtf, to make an alignment index. But if you want your alignment results to contain values for the control spikes, they are saying that you'll have to supplement the hg19 reference and gtf with sequences and annotation for the control spikes. If you don't ...
written 4 months ago by seidel6.3k
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Answer: A: Transcription factor enrichment analysis
... You can use the edgeR or DESEQ2 packages to find differentially expressed genes from your RNA Seq data, and you can use the GenomicRanges package to slice and dice your ChIP Seq data (assuming you've called peaks). However, you'll have to be a lot more specific with your question to get more specifi ...
written 6 months ago by seidel6.3k
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Answer: A: Editing header of a fasta file
... If your field of interest is always in the same position, you can try awk with the split() function and do something like the following: awk '{split($0,a,":"); if(a[10]) print ">"a[10]; else print; }' yourfile.fasta > newfile.fasta This translates to: split the input line by semicolon an ...
written 6 months ago by seidel6.3k
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Comment: C: how to determine the controls for cnv
... You need to improve this question. There aren't nearly enough details to understand how to formulate an answer. What kind of cnv analysis are you doing? What tools might you try? What is the experimental set up? What is the experimental system? What organism? ...
written 8 months ago by seidel6.3k
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Comment: C: How to annotate gene names for genomic coordinates?
... You mean instead of segments to genes, you want to know what genes appear within a given segment? The answer is above. Your cnv range (i.e. a segment) will return the index of the genes it overlaps. However, it can also be useful to turn the problem around, and use your genes as the query. i.e. for ...
written 8 months ago by seidel6.3k
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Comment: C: How to assign known subtype based on known gene signature
... What exactly is a subtype? Subtype of what? If I understand your question: you have three gene expression signatures - which means essentially that you have 3 vectors of numbers. You then have additional data. Each additional data set can be classified on whether or how well it matches any of the th ...
written 14 months ago by seidel6.3k
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Answer: A: How relevant, valuable, and important is Information Visualization nowadays in B
... Visualization can directly engage the decision making part of your brain, that is, *good* visualizations can. So from that perspective, a good visualization is essential. A picture that communicates a concept in data is very valuable, especially to the extent that it helps you *think* about that dat ...
written 14 months ago by seidel6.3k
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Answer: A: Visualizing hg19 and hg38 FPKMs in a single plot
... If you have FPKM values, then essentially the mapped reads have already been normalized to the appropriate gene structure, as Santosh notes in his comment "Note also that FPKM is normalized for transcript length". You can put them together in the same plot, but I would comment appropriately in the l ...
written 14 months ago by seidel6.3k
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Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
... The -h simply tells samtools to print out the header as well as the reads. Thus if you were to pipe this into another bam file (by also using the -b option) you have a fully formed bam file. ...
written 22 months ago by seidel6.3k

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Scholar 4 months ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
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