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: 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 19 days 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 24 days 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 24 days 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 3 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 3 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 10 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 11 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 12 months ago by Charles Warden5.0k
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Answer: A: convert BUSCO gff files to SNAP HMMs
... While I haven't directly used assemblage, I've done some testing with [MAKER][1], where I tended to get better results if I used protein / EST sequences (or an RNA-Seq *de novo* assembly) rather than starting with *de novo* gene predictions. Since it looks like assemblage is a modification of the M ...
written 12 months ago by Charles Warden5.0k
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Answer: A: Help for resource: Estimating age from 450k DNA methylation data
... The R code that you are supposed to run is within the Word / PDF files, which call the other files under "R Tutorials" At the beginning of the extracted R code, you'll need to define `dat0` as the beta matrix (such as `dat0 = read.table("probe_beta.txt",head=T, sep="\t")`) Also, at least with the ...
written 12 months ago by Charles Warden5.0k

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