User: shawn.w.foley

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shawn.w.foley1.2k
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Posts by shawn.w.foley

<prev • 132 results • page 1 of 14 • next >
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Comment: C: Interpretation of RNA seq pipeline in a paper
... I simply run `plot(density(log10(fpkm)))` in R. In my experience a bimodal curve is generated with a trough right near 1 FPKM. I always use this as a sanity check, I do have several datasets where the trough appears new 2 or 3 FPKM and adjust my filtering criteria accordingly. I've gone through th ...
written 4 months ago by shawn.w.foley1.2k
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Comment: C: Interpretation of RNA seq pipeline in a paper
... Just to clarify, the methods specify >2-fold change, which would be a |log2FC| > 1, not >2 (unless I misunderstood your answer). ...
written 4 months ago by shawn.w.foley1.2k
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Answer: A: Interpretation of RNA seq pipeline in a paper
... I'm not familiar with `edgeR` specifically, but I know that while `DESeq2` uses fits raw counts to a NB distribution when calculating differential expression, it includes a function to simply calculate and export RPKM/FPKM. ATPoint raises a good point about proceeding with caution, but my interpreta ...
written 4 months ago by shawn.w.foley1.2k
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Comment: C: cutoff for expressed genes in DESeq2
... My rule of thumb is FPKM >= 1, that being said I always generate a density plot of the FPKMs to view the distribution - in R I run `plot(density(log2(fpkm)))`. This (almost always) generates a bimodal distribution and I've found that 1 is very close to the trough of that distribution. However, th ...
written 5 months ago by shawn.w.foley1.2k
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Comment: C: GSEA: Does a gene set really have positive and negative enrichment scores?
... Rather than changing the sign of the p-value it's recommended to use the T-statistic. This number correlates to the p-value and is signed based on the fold change. My recommendation would be to perform a Hypergeometric test (similar to a GO term enrichment but using the gene sets of interest). I'd ...
written 6 months ago by shawn.w.foley1.2k
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Answer: A: GSEA: Does a gene set really have positive and negative enrichment scores?
... The short answer to your question is that if you have an equal distribution of up- and down-regulated genes within a gene set your NES (Normalized Enrichment Score) should be close to zero. The medium answer is that the NES is calculated from the ES (Enrichment Score), which is a rolling sum of the ...
written 6 months ago by shawn.w.foley1.2k
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Comment: C: How does one count unmapped transcripts ?
... Of that 30% how many are categorized as "too short"? @Charles Warden makes a good point about FastQC, you want to be certain this isn't a sequencing/library prep artifact before investing too much time into determining the source of these reads. ...
written 6 months ago by shawn.w.foley1.2k
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Comment: C: How to extract lncRNA from CPC2 output?
... Could you post a few lines so we can see what the output looks like? ...
written 6 months ago by shawn.w.foley1.2k
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Comment: C: How does one count unmapped transcripts ?
... If you have reads in a `.sam` file and you want to count their frequency you could make a quick `python` script: inFile = open('unmapped.sam','r') outFile = open('unmapped_read_count.txt','w') countDict = {} line = inFile.readline() #Remove header starting with @ symbol ...
written 6 months ago by shawn.w.foley1.2k
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Comment: C: How does one count unmapped transcripts ?
... It sounds like you know where these "external" genes have come from. If you have a `fasta` file with the sequence of these "external" genes then use that for mapping and see how many of the unmapped reads map to this second fasta/genome file. Depending on your mapping algorithm you might have an `u ...
written 6 months ago by shawn.w.foley1.2k

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Popular Question 4 months ago, created a question with more than 1,000 views. For Mutect2 "somatic" variants with resistant tissue culture lines
Appreciated 4 months ago, created a post with more than 5 votes. For A: Interpretation of RNA seq pipeline in a paper
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
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Scholar 6 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
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Scholar 7 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
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Scholar 9 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Scholar 9 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
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Scholar 9 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Middle author, but not first author projects. How would you approach this?
Scholar 10 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
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Popular Question 10 months ago, created a question with more than 1,000 views. For ChIP-seq differential binding with multiple replicates using MACS2 bdgdiff.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
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Scholar 11 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c

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