Moderator: Charles Warden
Charles Warden ♦ 5.6k
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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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... Good point - hopefully, this will be useful to Will :) ...
written 1 day ago by
Charles Warden ♦ 5.6k
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... It took me a second to realize the update was a comment (so, I don't know if the original user is still having an issue). However, for the sake of discussion, I'll throw some ideas out there:
**1)** I would like to see consistent signal from multiple probes / sites. So, if you have a way to deter ...
written 1 day ago by
Charles Warden ♦ 5.6k
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... While it is possible that there may in fact not be a consistent significance difference in methylation patterns, it is probably good to test out a few different options (especially if needing to avoid a false negative, where one particular method doesn't identify a particular difference, but another ...
written 6 days ago by
Charles Warden ♦ 5.6k
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... That is an interesting point.
Since I just looked into it more, perhaps some people would like to read more about Pre-2007 Illumina from a couple sources:
https://www.illumina.com/science/technology/next-generation-sequencing/illumina-sequencing-history.html
https://en.wikipedia.org/wiki/Illumina ...
written 7 days ago by
Charles Warden ♦ 5.6k
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... I don't think there is exactly one "best" motif prediction tool, but checking the results for a few programs may be useful.
I've sometimes found [i-cisTarget][1] and HOMER to be a good combination, but you could also try some of the tools from the [MEME Suite][2] (such as `meme-chip`, [web-based][3 ...
written 11 days ago by
Charles Warden ♦ 5.6k
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... I'm not sure what issues there could be with looking at coverage when the *de novo* annotations are from the same sample (compared to an independent set of annotations), but you could theoretically generate regions with [derfinder][1] (or do a reference-based *de novo* assembly, with a program like ...
written 14 days ago by
Charles Warden ♦ 5.6k
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... I'm sure if this is a tangent that should really be a separate thread for discussion, but I noticed that RepBase is having to [change it's method of support.][1]
Given that I would use [RepBase][2] for the command-line version of RepeatMasker, I am not sure how this affects things (and, in terms of ...
written 14 days ago by
Charles Warden ♦ 5.6k
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... In general, I would recommend that you test a few different methods for every project (such as [DESeq2][1] / [limma-voom][2] / [edgeR][3]), and see what seems to work best with your data (and/or if you get similar results).
As for the 1-versus-1 comparison, I would strongly recommending having bi ...
written 15 days ago by
Charles Warden ♦ 5.6k
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Comment:
C: log transformation of rpkm
... That is a good point that I didn't previously notice - if you have a panel of cell/tissue types, I could see how a z-score per-gene could be useful for identifying cell/tissue specific markers (that could also be true per-sample, which is what I thought was being asked about, but I don't believe I'v ...
written 21 days ago by
Charles Warden ♦ 5.6k
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Comment:
C: log transformation of rpkm
... While I have seen zFPKM used in at least one paper, I didn't realize that there was a [zFPKM][1] Bioconductor package. So, I am glad that Kevin pointed that out. However, that package says "Reference recommends using zFPKM > -3 to select expressed genes".
This alternative suggestion in the Bioc ...
written 22 days ago by
Charles Warden ♦ 5.6k
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