Moderator: Charles Warden

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Charles Warden4.8k
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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: 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 19 days 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 22 days 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 23 days 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 24 days 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 24 days 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 9 weeks 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 11 weeks ago by Charles Warden4.8k
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Answer: A: Peak Detection In Intergenic Regions In Rna-Seq Data
... If you are trying to find deferentially expressed regions that don't necessarily match annotated regions, I would recommend [derfinder][1]. It's pretty quick (at least compared to trying to perform a novel assembly with cufflinks), although I typically would at least start by focusing on annotatio ...
written 3 months ago by Charles Warden4.8k
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Comment: C: BWA-MEM using long PacBio reads
... Last time I checked, the acceptable output formats depended upon the input format - for example, I remember the change to not allow direct .sam file creation if the input is a .bam file. However, I have a version of BLASR installed in this [Docker image][1] that will at least work with the followin ...
written 4 months ago by Charles Warden4.8k
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Comment: C: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
... Actually, this is not correct: the example given for single-end data on the RSeQC website may be a little confusing because it is the opposite of what you typically observe in Illumina stranded libraries (but there is a verbal description of what the strand code represent). The counts are for reads ...
written 4 months ago by Charles Warden4.8k

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