User: mark.ziemann

gravatar for mark.ziemann
mark.ziemann1.1k
Reputation:
1,050
Status:
Trusted
Location:
Australia/Mebourne/Monash University
Website:
http://genomespot.blog...
Twitter:
@mdziemann
Last seen:
4 weeks ago
Joined:
3 years, 5 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 • 135 results • page 1 of 14 • next >
1
vote
1
answer
408
views
1
answers
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 10 weeks ago by mark.ziemann1.1k
0
votes
1
answer
232
views
1
answers
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 5 months ago by mark.ziemann1.1k
0
votes
1
answer
232
views
1
answers
Answer: A: Obtaining DEGs for bacterial RNA-sequencing study (levels of UV exposure)
... > 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 5 months ago by mark.ziemann1.1k
0
votes
0
answers
418
views
0
answers
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 9 months ago by mark.ziemann1.1k
0
votes
1
answer
697
views
1
answers
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 months ago by mark.ziemann1.1k
2
votes
2
answers
522
views
2
answers
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 months ago by mark.ziemann1.1k
2
votes
2
answers
522
views
2
answers
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 months ago by mark.ziemann1.1k
1
vote
0
answers
418
views
0
answers
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 months ago by mark.ziemann1.1k
3
votes
1
answer
408
views
1
answers
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 months ago by mark.ziemann1.1k
2
votes
1
answer
697
views
1
answers
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 months ago by mark.ziemann1.1k

Latest awards to mark.ziemann

Popular Question 7 months ago, created a question with more than 1,000 views. For Determine mutational profile from a BAM file?
Popular Question 7 months ago, created a question with more than 1,000 views. For Digital Expression Explorer
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: BWA MEM Algorithm
Guru 8 months ago, received more than 100 upvotes.
Scholar 9 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Scholar 9 months ago, created an answer that has been accepted. For A: The hard way?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Appreciated 10 months ago, created a post with more than 5 votes. For Digital Expression Explorer
Appreciated 10 months ago, created a post with more than 5 votes. For Digital Expression Explorer
Scholar 13 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Scholar 2.2 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Appreciated 2.4 years ago, created a post with more than 5 votes. For Digital Expression Explorer
Centurion 2.5 years ago, created 100 posts.
Scholar 3.0 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: JAVA and NGS
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: JAVA and NGS
Supporter 3.2 years ago, voted at least 25 times.
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: JAVA and NGS
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: JAVA and NGS
Rising Star 3.3 years ago, created 50 posts within first three months of joining.
Scholar 3.3 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Scholar 3.3 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1511 users visited in the last hour