User: mark.ziemann

gravatar for mark.ziemann
mark.ziemann1.0k
Reputation:
1,030
Status:
Trusted
Location:
Australia/Mebourne/Monash University
Website:
http://genomespot.blog...
Twitter:
@mdziemann
Last seen:
3 weeks ago
Joined:
2 years, 10 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 • 132 results • page 1 of 14 • next >
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Comment: C: WGBS - Methylation state at CpG to peak calls
... The methylKit documentation includes an example where methylation scores are calculated on tiles (1kbp) ...
written 8 weeks ago by mark.ziemann1.0k
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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 9 weeks ago by mark.ziemann1.0k
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Answer: A: Why do ribo-seq sequencing data have only a small proportion of uniquely mapped
... 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 9 weeks ago by mark.ziemann1.0k
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Answer: A: Why do ribo-seq sequencing data have only a small proportion of uniquely mapped
... 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 9 weeks ago by mark.ziemann1.0k
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Comment: C: WGBS - Methylation state at CpG to peak calls
... 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 9 weeks ago by mark.ziemann1.0k
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Answer: A: Looking for publicly available dataset.
... 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 9 weeks ago by mark.ziemann1.0k
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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 9 weeks ago by mark.ziemann1.0k
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Comment: C: Download ENCODE Project BED files using REST API
... Perfect! That's exactly what I was after! ...
written 5 months ago by mark.ziemann1.0k
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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 5 months ago by mark.ziemann1.0k
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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 6 months ago by mark.ziemann1.0k

Latest awards to mark.ziemann

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: BWA MEM Algorithm
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
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Appreciated 3 months ago, created a post with more than 5 votes. For Digital Expression Explorer
Scholar 6 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Scholar 20 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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