Moderator: swbarnes2

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swbarnes29.4k
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Posts by swbarnes2

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Answer: A: RNA-seq using DESeq2: quality control of replicates using PCA and heatmaps
... With only three replicates, you can't omit that sample based solely on your visualizations. Now, if the people who made the library have evidence that that sample didn't behave right, that would allow you to omit it, but for all you know, that variance (and PC2 is only 9%) is real. ...
written 1 day ago by swbarnes29.4k
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Answer: A: formatting issue in data for Upset plots
... Why don't your sets names match anything in the csv? I'd see if `nsets` works instead. ID's also try removing "Genome_location", and just having that be blank instead. R is generally happier with row names don't have a column header. ...
written 1 day ago by swbarnes29.4k
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Comment: C: IPA pathway for DESeq2 result
... SE stands for standard error. You don't want that. ...
written 3 days ago by swbarnes29.4k
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Answer: A: Trimmomatic couldn't generate output file
... For starters, I would not give your outputs the same name as your inputs! You need to keep inputs and outputs separate. The simplest explanation is that not a single one of your 20-027 reads passes your filter, so you just overwrote your original file with nothing. ...
written 6 days ago by swbarnes29.4k
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Comment: A: removal batch effect
... Also, note that for finding DE genes, the typical way to handle batches is **not** to alter the counts in anyway, but to leave them as they are, and include batch as an element of the design. ...
written 6 days ago by swbarnes29.4k
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Comment: C: BWA index is not working
... First things I'd check are that the formats of your fastqs and fastqs are okay. ...
written 7 days ago by swbarnes29.4k
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Comment: A: How to handle duplicate row names in R
... Go back and do things right with ensembl IDs. Those are always unique. ...
written 7 days ago by swbarnes29.4k
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Answer: A: Design and contrast matrices for including batch effect
... Illumina lanes generally do not add technical variance, so you shouldn't include them in the design. ...
written 7 days ago by swbarnes29.4k
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Answer: A: Unexpected gene polymorphism using Salmon-tximeta-DESeq2
... The annotation is what it is. Your first example is located on a real chromosome, the second is on a scaffold, FWIW. Just keep the ensemble IDs as the primary identifier all the way through. They are unique. ...
written 8 days ago by swbarnes29.4k
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Comment: C: Translating DNA into protein sequence considering ORF
... No one can troubleshoot without details of your code, and no one wants to write code for you. What exactly did you try? ...
written 12 days ago by swbarnes29.4k

Latest awards to swbarnes2

Commentator 3 days ago, created a comment with at least 3 up-votes. For C: All of the lines in my file are part of the header / no alignment section
Scholar 22 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 22 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Blast: Homology Or Similarity?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Blast: Homology Or Similarity?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 10 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Popular Question 11 weeks ago, created a question with more than 1,000 views. For DESeq2 multi-factor design
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Appreciated 3 months ago, created a post with more than 5 votes. For A: Blast: Homology Or Similarity?
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values

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