Moderator: Charles Warden

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Charles Warden4.7k
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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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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 4 weeks ago by Charles Warden4.7k
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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 6 weeks ago by Charles Warden4.7k
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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 11 weeks ago by Charles Warden4.7k
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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 3 months ago by Charles Warden4.7k
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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 3 months ago by Charles Warden4.7k
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Answer: A: BWA-MEM using long PacBio reads
... BWA is OK to use with CCS reads (preferably with at least 5 or 10 cycles), but that .fastq file seems quite large (and, unfortunately, unless you get a more raw data format, you can't use PacBio functions to define CCS reads). You could also use BLASR with a .fasta file, but the recommendation is t ...
written 3 months ago by Charles Warden4.7k
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Comment: C: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... CIBERSORT is designed for immune cell types. If you aren't specifically looking a mixture of immune cells, you might want to use a more generalized deconvolution strategy. If you are looking at bulk tumor expression, I would typically expect some sort of percent tumor value from the pathologist, w ...
written 3 months ago by Charles Warden4.7k
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Answer: A: HISAT2 or Tophat2
... I would say it depends on what you want to do with your data. I've sometimes found that the TopHat alignments work better than STAR alignments with some splicing analysis programs, possibly due to the format of the alignment. I would consider the run-time for TopHat to be sufficiently quick that y ...
written 3 months ago by Charles Warden4.7k
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Answer: A: RNA-SeQC does not calculate information about "Strand Specificity"
... You can see https://www.biostars.org/p/125344/ for more information about getting strand-specific information from RSeQC via infer_experiment.py. I'm not familiar with the report format that you provided, but I know that `infer_experiment.py` works. You can also double-check that chromosome format ...
written 3 months ago by Charles Warden4.7k
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Answer: A: How can I count one specific exon in RNA-seq data
... [DEXSeq][1] is a good suggestion. If you wanted to use [JunctionSeq][2] for splicing analysis, [QoRTs][3] can provide exon and splice junction counts. [1]: http://www.bioconductor.org/packages/2.10/bioc/html/DEXSeq.html [2]: https://bioconductor.org/packages/release/bioc/html/JunctionSeq.html ...
written 3 months ago by Charles Warden4.7k

Latest awards to Charles Warden

Scholar 4 weeks ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Your Favorite Bioinformatics Blog(S) (2013 Edition)
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 10 weeks ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Student 3 months ago, asked a question with at least 3 up-votes. For Gatk Error: Samfilereader Appears To Be Using The Wrong Encoding For Quality Scores
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Popular Question 4 months ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
Scholar 7 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 9 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 10 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 13 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Popular Question 18 months ago, created a question with more than 1,000 views. For Solution: Gatk Doesn't Recognize Karyotypic Ordering
Popular Question 20 months ago, created a question with more than 1,000 views. For How To Provide Reference Sequence Dictionary To Reordersam?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Finding New Cancer Biomarket/Drug Target From Ngs Analysis

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