Moderator: Charles Warden

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Charles Warden4.8k
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Duarte, CA
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@cwarden45
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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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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 7 weeks ago by Charles Warden4.8k
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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 10 weeks ago by Charles Warden4.8k
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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 weeks ago by Charles Warden4.8k
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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 3 months ago by Charles Warden4.8k
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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 3 months ago by Charles Warden4.8k
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Comment: C: differential exon usage
... [DEXSeq][1] uses a specialized scripts (**dexseq_prepare_annotation.py** and **dexseq_count.py**) to run HTSeq for exon counts. The manual mentions that you can use other read counting programs, but I would typically use those specifically designed for DEXSeq (using a GTF annotation file). Juncti ...
written 3 months ago by Charles Warden4.8k
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Answer: A: differential exon usage
... If you are looking at differential exon usage (for patient characteristics, tumor-normal, etc.), DEXSeq is a popular option. I happen to like [JunctionSeq][1] (which is based upon DEXSeq), which also includes splice sites (known junctions, and novel junctions between known exons) and an overall p-v ...
written 3 months ago by Charles Warden4.8k
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Answer: A: Is there any reason not to run RS_ReadsOfInsert?
... Depends upon the library size - I believe the default setting is 3 cycles, and using 5 or 10 cycles is a little better if defining CCS reads. However, I typically don't see CCS reads greater than a few kb in length. For genome assemblies, especially if you have 10+ kb segments of repetitive elemen ...
written 3 months ago by Charles Warden4.8k
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Answer: A: Why Different naming for this 450k CpG in IlluminaHumanMethylation450kanno.ilmn1
... The probe name indicates the methylation context, which can be either CpG or CpH (or a SNP probe with an rsID). For example, ch.9.7776528F has hg19 coordinate chr9:7786528. The probe is for a CpH on the forward strand, so that position is a "C" and the next nucleotide is an "A" (H=A, C, or T). In ...
written 5 months ago by Charles Warden4.8k
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Answer: A: Error correcting PacBio reads prior to alignment with bwa mem
... I would say it is OK to use CCS reads, where it might be a good idea to impose 5x or 10x cutoffs (the default is 3x). I'm not as certain about error-corrected subreads if the library size is too large to define CCS reads. I guess it should be OK, but I can't really provide you with evidence from 1 ...
written 5 months ago by Charles Warden4.8k

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