User: mark.ziemann

gravatar for mark.ziemann
mark.ziemann900
Reputation:
900
Status:
Trusted
Location:
Australia/Mebourne/Monash University
Website:
http://genomespot.blog...
Twitter:
@mdziemann
Last seen:
5 days, 23 hours ago
Joined:
2 years, 7 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

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Download ENCODE Project BED files using REST API
... Perfect! That's exactly what I was after! ...
written 12 weeks ago by mark.ziemann900
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Answer: A: Download ENCODE Project BED files using REST API
... I figured out how to do. If you use the web app search tool and click the download button, the "files.txt" will be downloaded. The 1st line of the file looked something like this. "https://www.encodeproject.org/metadata/type=Experiment&assay_title=ChIP-seq&target.investigated_as=transcripti ...
written 3 months ago by mark.ziemann900
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Download ENCODE Project BED files using REST API
... I'm trying to programmatically download all the narrowpeak bed files which match my search with the [ENCODE project web app][1]. I have tried instructions on the REST API using the python command as suggested by the documentation, but it doesn't seem to extract the download path. Maybe my search bri ...
python chip-seq written 3 months ago by mark.ziemann900
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Comment: C: Recommended program for evaluating aligner sensitivity
... I would go with Teaser if I were you. But if you have a specific need outside of the scope of it you could simulate the reads yourself (use [ART][1]) then use bedtools/awk to determine whether reads were mapped near the expected position with the expected orientation. This will at least get you some ...
written 3 months ago by mark.ziemann900
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Answer: A: Bismark Methyl-Seq Analysis
... Those bismark results would suggest that - Informatics pipeline is working well (result from group 2) - Bisulfite conversion is working well (result from group 1 CHG/CHH) - There is negligible CpG methylation (result from group 1 CpG) The 0.6% methylation percent is too close to the Illumina err ...
written 3 months ago by mark.ziemann900
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Answer: A: Recommended program for evaluating aligner sensitivity
... You could try [Teaser][1]. [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0803-1 ...
written 3 months ago by mark.ziemann900
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Answer: A: Total RNA-seq miRNA detection query
... Ribosomal RNA depleted RNA-seq won't capture small RNAs like microRNAs due to size. In RNA-seq, the RNA undergoes random priming for cDNA synthesis and there is a size selection step that excludes small fragments. To sequence small RNAs, a completely different library technique is used, which utilis ...
written 3 months ago by mark.ziemann900
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Answer: A: CNV tool for small sequences
... One solution could be to use a sliding window approach to compare coverage between samples. The window coordinates could be generated with BedTools and the reads quantified using Featurecounts. [Something similar has been discussed previously][1] as well as this [review article][2] . [1]: https: ...
written 3 months ago by mark.ziemann900
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Answer: A: Why does RNA sequencing data has Thymine as opposed to Uracil? Theoretically, it
... Because sequencing occurs after conversion to double stranded complementary DNA ([wikipedia][1]). Some systems like Oxford Nanopore are the exception because they read RNA directly [ONT website][2]. [1]: https://en.wikipedia.org/wiki/RNA-Seq [2]: https://nanoporetech.com/applications/rna ...
written 3 months ago by mark.ziemann900
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Comment: C: Workflow to store and integrate multiple NGS datasets for easy access and analys
... Keeping lists of genes in [GMT format][1] from each experiment is a lightweight approach. Differential RNA-seq data can be collapsed into rank files which can be analysed using spearman correlation. [1]: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Ge ...
written 3 months ago by mark.ziemann900

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Appreciated 18 days ago, created a post with more than 5 votes. For Digital Expression Explorer
Scholar 3 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
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Scholar 2.1 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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Scholar 2.5 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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