Moderator: Charles Warden

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Charles Warden5.0k
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I am a Bioinformatics Specialist at City of Hope, where I work in the Integrative Genomics Core doing microarray and high-throughput sequencing analysis.

Posts by Charles Warden

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Answer: A: mRNA-seq quality report (fastQC): Does it mean samples have adapters and should
... I think it is useful to check out the blog posts described by [genomax][1]. It's not unusual to have a relatively high duplicate rate for RNA-Seq data (although it can vary for different RNA-Seq protocols, and I would expect the duplicate estimation in aligned data to vary, at least to some extent, ...
written 24 days ago by Charles Warden5.0k
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Answer: A: calculating the fpkm from htseq counts
... While I often find it useful to use programs like [edgeR][1] / [DESeq2][2] / [limma-voom][3] for p-value calculations, I would say it is also useful to have log2(FPKM + 0.1) values for visualization (QC plots, heatmaps, etc). While the ways to calculate gene length can vary, the log-transformed exp ...
written 4 weeks ago by Charles Warden5.0k
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Answer: A: For Mean Expression/FC Calculations in scRNA-seq, should I use All cells or only
... It is probably a good idea to do some extra QC filtering (such as for cells with a minimum number of covered genes, and cells with a sufficiently low percentage of mitochondrial reads), but the criteria that can/should be applied will likely vary between projects. I'm not sure how easy it is to do ...
written 9 weeks ago by Charles Warden5.0k
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Answer: A: Analysis with no Differentially Expressed Genes?
... It is definitely possible to have genes identified with a 3 x 3 comparisons, but I'm not sure of how clear the Ti50 effect is. I would usually expect limma to be a little more sensitive than the built-in R functions (like `aov()` for ANOVA and `lm()` for linear-regression), although some of those p ...
written 10 weeks ago by Charles Warden5.0k
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Answer: A: Differential ChIP-Seq Analysis
... Yes - for a particular set of peaks, you can quantify counts (with htseq-count, featureCounts, etc.) and then use DESeq2/edgeR for p-value calculations. ...
written 10 weeks ago by Charles Warden5.0k
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Comment: C: RNA-Seq database for immune cells
... This is a good suggestion! If looking for raw ImmGen RNA-Seq data, the GEO entry (and link to SRA reads) is [GSE109125][1]. This is for mouse sorted cells. While I should probably learn more about ImmGene / Gene Skyline, I didn't see RNA-Seq data from human cells. [1]: https://www.ncbi.nlm.nih ...
written 5 months ago by Charles Warden5.0k
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Answer: A: RNA-Seq database for immune cells
... Immune cell signatures defined from microarray datasets have been applied to RNA-Seq data, so it may still be worth considering the microarray gene expression datasets. While I would also be curious to know about comparable RNA-Seq datasets, you could keep an eye on citations for these fairly popul ...
written 5 months ago by Charles Warden5.0k
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Comment: C: Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
... Yes - MATS will work without replicates. If you do have replicates, [JunctionSeq][1] is also a relatively new option that I currently rank as my top choice for splicing analysis. [1]: http://hartleys.github.io/JunctionSeq/ ...
written 12 months ago by Charles Warden5.0k
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Comment: C: What is a typical workflow to correlate methylation and expression data?
... Lowering the delta-beta cutoff will only help if the methylated thresholds are also changed. You could try setting both methyl.cutoff and unmethyl.cutoff equal to 0.3, or disable the use of methylated thresholds by setting unmethyl.cutoff=1 and methyl.cutoff=0. Yes - in terms of posting etiquette, ...
written 13 months ago by Charles Warden5.0k
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Answer: A: How can we find the 16S rRNA sequence of an organism from NCBI?
... In most cases, it is difficult to confidently resolve classifications for 16S data at the species or sub-species level. So, if you were specifically interested in types of *Staphylococcus aureus*, it might be best to use a different marker (which you could define from comparing whole genome sequenc ...
written 13 months ago by Charles Warden5.0k

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