User: mark.ziemann
mark.ziemann • 1.1k
- Reputation:
- 1,080
- Status:
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- Location:
- Australia/Mebourne/Geelong/Deakin
- Website:
- http://genomespot.blog...
- Twitter:
- @mdziemann
- Last seen:
- 16 hours ago
- Joined:
- 3 years, 10 months ago
- Email:
- m***********@gmail.com
I'm a researcher and lecturer at Deakin University, Australia. I use Next Generation Sequencing to study epigenetics in a range of human diseases.
Posts by mark.ziemann
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... Have you tried a simulation study to see which mapper is better able to deal with the high divergence? You could use [Simulome][1] to generate a reference sequence in FASTA format then simulate Illumina read pairs with [ART][2].
[1]: https://academic.oup.com/bioinformatics/article/33/12/1876/29823 ...
written 11 weeks ago by
mark.ziemann • 1.1k
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... > combine, then adjust.
>
> Fisher's method has certain assumptions about what the p-value is that
> will almost certainly be violated if you do multiple-testing
> correction first.
Originally posted by [Brent P][1]
[1]: https://www.biostars.org/p/84242/ ...
written 4 months ago by
mark.ziemann • 1.1k
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... Best to open a new question - I'm sure the community can help you with your request :) ...
written 7 months ago by
mark.ziemann • 1.1k
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... > 1) Are there any other recommended ways to try to determine which
> genes in a bacteria are "differentially expressed" in response to a
> treatment (here UV radiation)? Is RNA-sequencing the preferred way to
> do this? I am only asking because you stated that "most reads will map
> ...
written 10 months ago by
mark.ziemann • 1.1k
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... > 1) Is RNA-sequencing possible for bacteria?
Yes. Although most reads will map to the highly abundant rRNA. DESeq2 will work just fine.
> 2) Would methylation studies be of interest for these 3 different
> levels of UV radiation in a bacteria? What type of R package would be
> useful ...
written 11 months ago by
mark.ziemann • 1.1k
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... The methylKit documentation includes an example where methylation scores are calculated on tiles (1kbp) ...
written 14 months ago by
mark.ziemann • 1.1k
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Comment:
C: Cut-off for genesets in GSEA
... Oh OK, so you want to exclude gene sets with fewer than 10 or 15 members. They are just unreliable.
You shouldn't exclude gene sets because they have more than X members. This GSEA feature is puzzling to me. I set the larger threshold to something really large like 5000. You can count the number of ...
written 14 months ago by
mark.ziemann • 1.1k
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... You're correct in that it could just be short length or rRNA. It is relatively easy to check the following:
1. Screen rRNA content http://genomespot.blogspot.com.au/2015/08/screen-for-rrna-contamination-in-rna.html
2. Simulate cDNA reads of the different lengths and determine the proportion that ...
written 14 months ago by
mark.ziemann • 1.1k
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... You're correct in that it could just be short length or rRNA. It is relatively easy to check the following:
1. Screen rRNA content http://genomespot.blogspot.com.au/2015/08/screen-for-rrna-contamination-in-rna.html
2. Simulate cDNA reads of the different lengths and determine the proportion that ...
written 14 months ago by
mark.ziemann • 1.1k
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... some tips here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165320/
I have used methylkit and it appears to work well. http://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html ...
written 14 months ago by
mark.ziemann • 1.1k
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For C: Problem with creating GSEA rank file
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