User: mark.ziemann
mark.ziemann • 1.2k
- Reputation:
- 1,190
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- Location:
- Australia/Mebourne/Geelong/Deakin
- Website:
- http://genomespot.blog...
- Twitter:
- @mdziemann
- Last seen:
- 2 hours ago
- Joined:
- 4 years, 5 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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... Would it be informative to calculate the GC content of the reads themselves? ...
written 23 days ago by
mark.ziemann • 1.2k
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Comment:
C: How to do the WGCNA in R
... In addition to the reference manual, you might want to see if you can follow the tutorial with cancer data [here][1] to learn how it works then substitute you own data.
[1]: https://bioconductor.org/packages/devel/bioc/vignettes/CVE/inst/doc/WGCNA_from_TCGA_RNAseq.html ...
written 25 days ago by
mark.ziemann • 1.2k
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... I experienced the same thing just now on a not so well patched computer running an older version (R3.4.4/fgsea_1.0.2/BiocParallel_1.8.2) but tried it on another computer that I keep better updated (R3.5.2/fgsea_1.8.0/BiocParallel_1.8.2) and it worked. My advice would be to upgrade your R installatio ...
written 6 months ago by
mark.ziemann • 1.2k
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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 9 months ago by
mark.ziemann • 1.2k
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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 11 months ago by
mark.ziemann • 1.2k
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... Best to open a new question - I'm sure the community can help you with your request :) ...
written 14 months ago by
mark.ziemann • 1.2k
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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 18 months ago by
mark.ziemann • 1.2k
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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 18 months ago by
mark.ziemann • 1.2k
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... The methylKit documentation includes an example where methylation scores are calculated on tiles (1kbp) ...
written 21 months ago by
mark.ziemann • 1.2k
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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 21 months ago by
mark.ziemann • 1.2k
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20 days ago,
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For A: tRNA expression analysis from RNA-Seq
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For A: Get CDS from WGS fasta OR download just CDS
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For A: tRNA expression analysis from RNA-Seq
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For C: Problem with creating GSEA rank file
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For A: Get CDS from WGS fasta OR download just CDS
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For A: tRNA expression analysis from RNA-Seq
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