User: Charles Warden

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

However, the feedback that I provide represent my own personal opinions.

Posts by Charles Warden

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Forum: How to Fairly Represent and Interpret Direct-To-Consumer Ancestry Results?

... For [my own ancestry results]( http://cdwscience.blogspot.com/2019/08/genome-wide-broad-level-super.html), I would say that the broad-level assignments (like the [1000 Genomes super-populations]( https://www.internationalgenome.org/category/population/)) were accurate but I had some concerns about s ...

chromosome+painting ancestry forum admixture written 12 days ago by Charles Warden ♦ 7.6k

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Answer: A: How to properly identify most likely species from small amplicon sequences?

... I have only worked with a somewhat limited number of larger samples. However, to me, the main difference with having PacBio full length 16S sequences (V19) versus shorter MiSeq (V13, V34, V45, etc.) or HiSeq sequences (V3, V4, V5, etc.) was the ability to have more genera assignments for a larger f ...

written 14 days ago by Charles Warden ♦ 7.6k

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Answer: A: Skewed beta-distribution from Methylation EPIC array data

... I think the comments pretty much answer the question, but I would recommend using a different normalization. Sometimes, popular normalization can cause problems that would be obvious upon visual inspection of the density distributions (like you have shown). So, you should try to figure out what wo ...

written 19 days ago by Charles Warden ♦ 7.6k

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Answer: A: What is the current standard for HLA allele typing prediction from SNP data?

... I am not sure if "standard" is exactly the right word, even though I can imagine that is what a lot of people may use. However, you can see the results and concordance for my own SNP chip and sequencing data (with 2 methods each; [SNP2HLA][1] and [HIBAG][2] for **SNP chip**; [bwakit][3] and [HLAmin ...

written 22 days ago by Charles Warden ♦ 7.6k

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Answer: A: Studying for a Bioinformatics degree

... While not a perfect solution, I have some notes on on-line courses here: http://cdwscience.blogspot.com/2019/12/experiences-with-on-line-courses.html If you don't have any experience, I think an on-campus degree might have advantages. **If you are talking about a Bachelor's degree, then I would p ...

written 26 days ago by Charles Warden ♦ 7.6k

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Answer: A: How to generate CpG REGIONs file to run DMR analysis with methylkit?

... If this is human, perhaps you can consider the UCSC CpG Islands (and you can get some gene mappings through Bioconductor)? The RRBS coverage may also tend to be in certain blocks, so you could also use distance to the gene. However, I think that knowing about the CpG Islands (or more specific boun ...

written 26 days ago by Charles Warden ♦ 7.6k

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Comment: C: HLA and Haploview

... To be honest, I am not sure if I have created a plot for Haploview. However, I describe some analysis of my HLA genes here: http://cdwscience.blogspot.com/2019/08/predicting-hla-types-for-array-and-high.html Also, I think you may want to move this question as a comment on my answer (rather than a ...

written 5 weeks ago by Charles Warden ♦ 7.6k

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Comment: C: AB1 to FASTQ

... The quality score was actually defined for Sanger reads before Illumina reads. However, Illumina has also changed the quality offset over time. This may also be a bit like the quality score distribution looking noticeably different for Illumina versus PacBio CCS reads. So, you may need to use you ...

written 5 weeks ago by Charles Warden ♦ 7.6k

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Comment: C: AB1 to FASTQ

... You can extract the quality scores in BioPython: seqHandle = SeqIO.parse("file.ab1", "abi") for seq in seqHandle: seqName = seq.id seqStr = str(seq.seq) seqQual = seq.letter_annotations["phred_quality"] You probably also want to do some additional trimming, and I would definitely encoura ...

written 5 weeks ago by Charles Warden ♦ 7.6k

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Answer: A: HLA and Haploview

... While there may be advantages to visualizing the HLA region in Haploview, I would typically use an alternate set of references for analyzing the individual HLA genes. So, I apologize that this doesn't directly answer your question, but it is possible there may be additional complications with this ...

written 5 weeks ago by Charles Warden ♦ 7.6k

Latest awards to Charles Warden

Scholar 19 days ago, created an answer that has been accepted. For A: Validating Predictions Of Small Insertions / Deletions

Scholar 25 days ago, created an answer that has been accepted. For A: Validating Predictions Of Small Insertions / Deletions

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: splice site mutations

Scholar 8 weeks ago, created an answer that has been accepted. For A: Publications for individualized medicine in cancer by whole genome, exome or tra

Oracle 10 weeks ago, created more than 1,000 posts (questions + answers + comments).

Scholar 11 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 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

Scholar 4 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 5 months ago, created a question with more than 1,000 views. For Memory Allocation for VarScan

Appreciated 5 months ago, created a post with more than 5 votes. For A: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data

Appreciated 6 months ago, created a post with more than 5 votes. For A: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data

Teacher 6 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 6 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 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

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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 8 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

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Scholar 11 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

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Scholar 11 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 12 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

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