Moderator: Charles Warden

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Charles Warden7.6k
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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.

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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k
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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 Warden7.6k

Latest awards to Charles Warden

Scholar 19 days ago, created an answer that has been accepted. For A: Validating Predictions Of Small Insertions / Deletions
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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: splice site mutations
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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
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