User: mark.ziemann

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mark.ziemann1.2k
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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

<prev • 143 results • page 1 of 15 • next >
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Comment: C: Extract flanking regions from bam files based on coverage threshold
... 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.ziemann1.2k
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Answer: A: Is BWT algorithm suitable for all types of alignment task?
... 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.ziemann1.2k
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Comment: C: Extract flanking regions from bam files based on coverage threshold
... 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.ziemann1.2k
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Comment: C: Detecting GC Bias in Transcriptomes (RNA-seq)
... Would it be informative to calculate the GC content of the reads themselves? ...
written 4 months ago by mark.ziemann1.2k
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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.ziemann1.2k
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Answer: A: fgsea tutorial issue with BiocParallel
... 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.ziemann1.2k
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Comment: C: Choosing the best alignment or aligner
... 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.ziemann1.2k
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Answer: A: Meta-Analysis p-value combining and adjusting
... > 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.ziemann1.2k
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Comment: C: Looking for publicly available dataset.
... Best to open a new question - I'm sure the community can help you with your request :) ...
written 18 months ago by mark.ziemann1.2k
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Comment: C: Obtaining DEGs for bacterial RNA-sequencing study (levels of UV exposure)
... > 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.ziemann1.2k

Latest awards to mark.ziemann

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Appreciated 9 months ago, created a post with more than 5 votes. For A: JAVA and NGS
Scholar 9 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Problem with creating GSEA rank file
Popular Question 23 months ago, created a question with more than 1,000 views. For Determine mutational profile from a BAM file?
Popular Question 23 months ago, created a question with more than 1,000 views. For Digital Expression Explorer
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: BWA MEM Algorithm
Guru 2.0 years ago, received more than 100 upvotes.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Scholar 2.1 years ago, created an answer that has been accepted. For A: The hard way?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
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Appreciated 2.2 years ago, created a post with more than 5 votes. For Digital Expression Explorer
Scholar 2.4 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Scholar 3.5 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Appreciated 3.6 years ago, created a post with more than 5 votes. For Digital Expression Explorer
Centurion 3.8 years ago, created 100 posts.
Scholar 4.3 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: JAVA and NGS
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Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: JAVA and NGS

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