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User: shawn.w.foley

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Posts by shawn.w.foley

<prev • 12 results • page 1 of 2 • next >
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ChIP-seq differential binding with multiple replicates using MACS2 bdgdiff.
... Hello, I'm trying to perform a differential binding ChIP-seq experiment and am struggling with the best way to incorporate my replicates using MACS2. I have two sets of samples, control rep 1-3 and control input, as well as treated rep 1-3 and treated input. If I run macs2 callpeak as recommended I ...
bdgdiff macs2 chip-seq written 4 months ago by shawn.w.foley • 90
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Comment: C: Analyzing RNA-seq without replicates
... Thank you for the help, this input has been great! DESeq2 will also allow me to calculate the expression fold changes for each individual patient pre- and post-treatment. I want to confirm that I should not put any weight into the reported p-values/FDRs for the individual patients. Instead I shoul ...
written 5 months ago by shawn.w.foley • 90
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Analyzing RNA-seq without replicates
... Hello, I'm currently analyzing an RNA-seq experiment consisting of clinical patient samples pre- and post-treatment, for individuals that had no response (NR, n=6), partial response (PR, n=4), or complete response (CR, n=2) to our compound. Unfortunately, no replicates were collected for each indiv ...
cufflinks isoem2 deseq2 isode2 rna-seq written 5 months ago by shawn.w.foley • 90 • updated 5 months ago by i.sudbery • 2.4k
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Comment: C: How to find the gene structure of a gene?
... Can you give more detail about what you're looking for? Are you annotating genes de novo and trying to predict structure? Does structure mean where is the CDS? Are you interested in each exon, and each UTR? Is this a novel organism or are you looking for annotation files? ...
written 6 months ago by shawn.w.foley • 90
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Comment: C: R DESeq: What exactly is Variance Stabilizating Transformation?
... I'm sure you've found the answer by now, but to take an rlog you can run: `rlogTransformation(cds)` or simply `rlog(cds).` ...
written 6 months ago by shawn.w.foley • 90
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Answer: A: How do strand specific sequencing protocols work?
... I personally have used two different methods for the generation of strand-specific RNA-seq libraries. 1) We used mutated RNA ligases to directly ligate the adapters onto the RNA before RT-PCR. In this technique we use one enzyme that specifically ligates a DNA adapter to the 3' end of the RNA, and ...
written 6 months ago by shawn.w.foley • 90
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Answer: A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
... You're correct that technical replicates are not necessary for RNA-seq, however biological replicates are always necessary for statistical analyses. Without replicates you cannot have any p-values. A technical replicate in RNA-seq, in my experience, refers to taking one tube of RNA and then making ...
written 6 months ago by shawn.w.foley • 90
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Answer: A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
... After more searching I found the answer to my question, I'm posting it here in case someone needs to do a similar analysis in the future. The answer to this question is absent from the crlmm genotyping vignette, however if you look through the full vignette [here][1], you can find the appropriate an ...
written 7 months ago by shawn.w.foley • 90
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How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or crlmm?
... Taking publicly available Affy SNP6.0 data, I am trying to find the normalized signal for each probe. I've used both the "oligo" and "crlmm" from Bioconductor, and these generate a SnpSuperSet variable where I can then use calls(x) to find the genotype (AA=1, AB=2, or BB=3) or I can use confs(x) to ...
bioconductor crlmm snp oligos written 7 months ago by shawn.w.foley • 90
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Comment: C: When performing Fisher's exact test, should I consider all annotated or all dete
... This looks perfect, thank you! ...
written 7 months ago by shawn.w.foley • 90

Latest awards to shawn.w.foley

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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
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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