Moderator: Charles Warden
Charles Warden ♦ 7.9k
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- 7 years, 4 months ago
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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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... 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 Warden ♦ 7.9k
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... 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 Warden ♦ 7.9k
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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 Warden ♦ 7.9k
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... 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 Warden ♦ 7.9k
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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 Warden ♦ 7.9k
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... 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 Warden ♦ 7.9k
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... Also, I can see the pictures now. So, thank you for fixing that. ...
written 3 months ago by
Charles Warden ♦ 7.9k
1
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... 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 Warden ♦ 7.9k
3
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... 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 Warden ♦ 7.9k
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... 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 Warden ♦ 7.9k
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For A: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
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