User: mark.ziemann
mark.ziemann • 1.2k
- Reputation:
- 1,200
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- Location:
- Australia/Mebourne/Geelong/Deakin
- Website:
- http://genomespot.blog...
- Twitter:
- @mdziemann
- Last seen:
- 2 hours ago
- Joined:
- 4 years, 9 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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... Most SNP callers like GATK, VarScan, BCFtools, will provide a coverage for each SNP that you can filter on. After filtering for SNPs that satisfy your threshold, you can use `bedtools slop` to expand them by 50 bases and supply these regions to `samtools mpileup`. ...
written 14 days ago by
mark.ziemann • 1.2k
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... BWT based aligners have been applied to most problems already, namely BWA for DNA, Olego for RNA and Biscuit for bisulfite sequencing. STAR is an RNA aligner that uses a large suffix array. There are other tools like kallisto that compare kmer content to perform mapping. ...
written 16 days ago by
mark.ziemann • 1.2k
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... One way to do this would be to use `samtools mpileup` supplying a list of SNP regions as an option, then filter the output based on your minimum coverage requirement.
Related: [https://www.biostars.org/p/93673/#93676][1]
[1]: https://www.biostars.org/p/93673/#93676 ...
written 16 days ago by
mark.ziemann • 1.2k
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... Would it be informative to calculate the GC content of the reads themselves? ...
written 4 months 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 4 months 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 9 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 13 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 14 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 18 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 21 months ago by
mark.ziemann • 1.2k
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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 A: tRNA expression analysis from RNA-Seq
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For C: Problem with creating GSEA rank file
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For Determine mutational profile from a BAM 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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For A: Get CDS from WGS fasta OR download just CDS
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