Moderator: Charles Warden

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Charles Warden7.9k
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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

<prev • 1,043 results • page 1 of 105 • next >
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Answer: A: Can I add more than one effect (example: treatment and sex) to cuffdiff ?
... I don't believe that you can include a second variable for cuffdiff. However, you can do so for [edgeR][1], [limma-voom][2], [DESeq2][3], and even a regular ANOVA or linear regression. In fact, you might find those strategies advantageous over cuffdiff (even though cufflinks can be useful for refe ...
written 7 days ago by Charles Warden7.9k
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Comment: C: Statistical test for DMR annotation?
... Hi Amit, I apologize that this quite a while after your original post. These would be my thoughts: **1)** The situation might be different for Whole Genome Bisulfite Sequencing (WGBS), but I think targeted sequence has some rough targeted boundaries to begin with. So, I think one problem could b ...
written 15 days ago by Charles Warden7.9k
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Comment: C: How to count SNPs, InDels
... Hi - I think you meant this as a comment for my other answer. Also, I think you might be referring to this blog post: http://cdwscience.blogspot.com/2019/05/precisionfda-and-custom-scripts-for.html My sense is that it helps to be able to visually inspect variation calls, and I am not sure I would ...
written 4 weeks ago by Charles Warden7.9k
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Comment: C: how to combine methylation information from different platform?
... There are CpG sites outside of CpG islands. So, 100% of the sites shouldn't be covered by RRBS. However, that percent does sound low. Unless you have *n* samples and you are asking how many RRBS sites are covered in 100% of your *n* samples (and *n*>20 or *n*>100), I think it should be high ...
written 7 weeks ago by Charles Warden7.9k
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Answer: A: How to count SNPs, InDels
... You can also use the summary from `bcftools stats` to answer this question. http://samtools.github.io/bcftools/bcftools.html#stats ...
written 8 weeks ago by Charles Warden7.9k
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Comment: C: How to do DMR analysis with BiSeq (for RRBS methylation data)?
... To be honest, I preferred both methylKit and COHCAP over BiSeq. I developed COHCAP, but I acknowledge that setting things up might be a bit of a challenge (and my ability to support using the code may be a limited, especially on certain weeks). So, I think [methylKit][1] may be easier to use, and ...
written 3 months ago by Charles Warden7.9k
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Comment: C: Help with my differential expression analysis (homework)
... Also, I can see the pictures now. So, thank you for fixing that. ...
written 3 months ago by Charles Warden7.9k
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Comment: C: Help with my differential expression analysis (homework)
... That is a good catch. If you have a genome reference, you should use a program like TopHat2, STAR, HISAT2, etc. If you have a transcriptome alignment, then you could use Bowtie2 or BWA (or quantify reads without aligning, with a program like Salmon or Kallisto). That said, my understanding that t ...
written 3 months ago by Charles Warden7.9k
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Answer: A: Help with my differential expression analysis, I am an inexperienced student in
... In general, I don't think Biostars is supposed to be providing support for specific homework questions. I can't see the images that you tried to provide, but what you quantify depends upon what annotations you use. Also, there are separate kits for miRNA-Seq, and even that may require additional p ...
written 3 months ago by Charles Warden7.9k
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Comment: C: Differential DNA methylation for each sample using Illumina HumanMethylation450
... I think something doesn't seem right, but it is hard for me to say for certain. For the site test, I believe minfi is using a [logit transform][1] (or some sort of transform to make the data look more normally distributed) and limma. While this has some advantages, you can also miss some sites tha ...
written 3 months ago by Charles Warden7.9k

Latest awards to Charles Warden

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Teacher 23 days ago, created an answer with at least 3 up-votes. For A: splice site mutations
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Scholar 8 months ago, created an answer that has been accepted. For A: Validating Predictions Of Small Insertions / Deletions
Scholar 8 months ago, created an answer that has been accepted. For A: Validating Predictions Of Small Insertions / Deletions
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: splice site mutations
Scholar 9 months ago, created an answer that has been accepted. For A: Publications for individualized medicine in cancer by whole genome, exome or tra
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