User: mark.ziemann
mark.ziemann • 1.0k
- Reputation:
- 1,040
- Status:
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- Location:
- Australia/Mebourne/Monash University
- Website:
- http://genomespot.blog...
- Twitter:
- @mdziemann
- Last seen:
- 2 weeks, 1 day ago
- Joined:
- 3 years, 2 months ago
- Email:
- m***********@gmail.com
I'm a researcher at Monash University in Melbourne. I use Next Generation Sequencing to study epigenetics in a range of human diseases.
Posts by mark.ziemann
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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 12 weeks ago by
mark.ziemann • 1.0k
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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 12 weeks ago by
mark.ziemann • 1.0k
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... The methylKit documentation includes an example where methylation scores are calculated on tiles (1kbp) ...
written 6 months ago by
mark.ziemann • 1.0k
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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 6 months ago by
mark.ziemann • 1.0k
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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 6 months ago by
mark.ziemann • 1.0k
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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 6 months ago by
mark.ziemann • 1.0k
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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 6 months ago by
mark.ziemann • 1.0k
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... 2 good options:
recount2 https://jhubiostatistics.shinyapps.io/recount/
ARCHS4 http://amp.pharm.mssm.edu/archs4/
Also many GEO series include count matrices although these are generated by various pipelines. ...
written 6 months ago by
mark.ziemann • 1.0k
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Comment:
C: Cut-off for genesets in GSEA
... Hi Shamim, the preranked file should contain differential expression scores for all detected genes. This is normally 10 to 20 thousand genes. Do not exclude genes with FDR>0.05 ...
written 6 months ago by
mark.ziemann • 1.0k
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... Perfect! That's exactly what I was after! ...
written 10 months ago by
mark.ziemann • 1.0k
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