Moderator: Charles Warden

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Charles Warden5.9k
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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.

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

Posts by Charles Warden

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Comment: C: RNA-Seq time series analysis using a DESeq2 spline approach yields far too many
... With all due respect, I disagree - I think 15,000 differentially expressed genes seems high (I usually expect getting closer to 1,500 genes is better for specific enrichment). In general, I think you need to test and critically assess different methods for each project. The context is a little dif ...
written 5 hours ago by Charles Warden5.9k
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Answer: A: HLA analysis using SNP2HLA
... I would have to couple check the output files on my home computer, but I think there should be a way to define your top 2 haplotypes. For example, I have these comparisons with different HLA programs for my own genome data (underneath the huge "23andMe versus Genes for Good" Venn Diagram): https:/ ...
written 5 hours ago by Charles Warden5.9k
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Comment: C: Is Dell Precision mobile workstation suitable for bioinformatics/NGS analysis
... If your lab has a shared network folder, maybe the hard drive space isn't a huge issue. For example, I'm guessing sequencing reads are originally being saved in a place that is accessible to your lab and/or institute compute resources (not just your local computer)? For example, you'll need to hav ...
written 5 hours ago by Charles Warden5.9k
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Answer: A: When to remove duplicates using deduplication in Exome-Seq
... I would typically expect duplicates to be removed for Exomes, but it is hard to say what is absolutely right for all variants (for all target designs). For example, you may notice weird behavior in GATK with very high coverage (say, >1000x or >10000x) regions, and/or shifts in variant frequen ...
written 5 hours ago by Charles Warden5.9k
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Comment: C: Using linear regression to accounting for confounding variables in gene expressi
... Taking the time to critically assess papers (and answer questions about your own work) is important, and suspect this requires people to be able to study a limited number of topics in-depth. In other words, I am not immediately sure what to say about this specific paper. However, if I have a chanc ...
written 1 day ago by Charles Warden5.9k
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Answer: A: Bioinformatics Master thesis
... If possible, I think it would be best if you could have first-hand experience before making long-term decisions. This may not always be possible (and people can get hired in areas other than what they have been trained), but I would at least try to see what you can to in terms of assessing your abi ...
written 1 day ago by Charles Warden5.9k
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Answer: A: edgeR batch effect
... Maybe you should check out this thread? https://www.biostars.org/p/356810 In general, I think it would be best if you used something other than the MDS plot to be confident the batch was appropriately adjusted, without over-fitting and/or over-correction. However, I think the individual feedback ...
written 1 day ago by Charles Warden5.9k
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Answer: A: Is it fine to run SVM on RNA-seq read counts?
... **If you pick the genes/features using your full set of samples, you won't independent training / validation datasets** (which I would argue is why you would test predictability with a machine learning method, versus a statistical test in a smaller set of samples). If you are using another dataset ...
written 1 day ago by Charles Warden5.9k
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Answer: A: FastQC report analysis
... I think it is better to visually review the FastQC results to make your assessment. For example, if you look at enough categories, I think you will encounter some with "warning" or "fail" status, but you may still be able to get useful results from the data. FastQC has some known sequences that it ...
written 1 day ago by Charles Warden5.9k
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Answer: A: Mapping transcripts to genome
... I think I had to change some parameters (and also have manual review of the annotation) to get a reasonable result. However, if your goal is genome annotation, perhaps you can see if [MAKER][1] can help? This can use *de novo* predictions in addition to RNA-Seq data (I think that was primarily thr ...
written 1 day ago by Charles Warden5.9k

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