User: mark.ziemann

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mark.ziemann1.3k
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Location:
Australia/Mebourne/Geelong/Deakin
Website:
http://genomespot.blog...
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@mdziemann
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Last seen:
2 weeks, 1 day ago
Joined:
5 years, 11 months ago
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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. Maintainer of the DEE2 RNA-seq database: http://dee2.io

Posts by mark.ziemann

<prev • 160 results • page 1 of 16 • next >
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Comment: C: Tool/Pipeline to get annotations from RNA-Seq
... Some additional information would be useful. What species are you working on? Is there a good quality reference genome and gene annotations already or are you doing this de novo? Do you have a set of transposon sequences already that you are trying to quantify or do you need to characterise these de ...
written 11 weeks ago by mark.ziemann1.3k
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DMR calling for EWAS meta-analysis
... Hi Biostars, I'm looking for a package/tool that can perform DMR calling of Infinium array data after meta-analysis. All the packages I've seen so far (eg:DMRcate and bumphunter) require the original matrices of m- or beta-values which won't work for us. We tried combp from the ENmix package but t ...
dna methylation epigenetics dmr calling written 3 months ago by mark.ziemann1.3k • updated 11 weeks ago by Biostar ♦♦ 20
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Answer: A: Number of replicates in each group in RNA seq
... The statistical packages like DESeq2 should be able to manage with unbalanced replicate numbers as long as the numbers are not too low. Downsampling shouldn't be required. If you still have a doubt, you can ask on the Bioconductor forum [1] tagging the tool that you are using. 1. https://support.b ...
written 4 months ago by mark.ziemann1.3k
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Answer: A: CAST/EiJ mouse strain Reference Transcriptome (do we have one? if not, how to bu
... If you visit the Ensembl FTP site [1] and search for "CAST/EiJ" you will see there is a build for this strain. Similarly there are many other mouse strains also included. The "cDNA" fasta can be used for Salmon and Kallisto. Just take note that this will not include non-coding RNAs. I you want those ...
written 4 months ago by mark.ziemann1.3k
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Comment: C: Any reason for higher reported levels of non-CG methylation when analysing non-d
... It could be: 1. Difference in bisulfite conversion efficiency 2. Overall error rate differences in these seq runs - if you could obtain the phi-x from those runs you could check the error rates precisely 3. Something related to the alignment search space being twice as large for non-directional ...
written 11 months ago by mark.ziemann1.3k
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Comment: C: Best way to find all downloadable publicly available raw fastq files from SRA/GE
... Are you able to use the SRA search and send the results to SRA run selector? Then you can collect a list of SRA runs (start with SRR.ERR.DRR) which you can pass to prefetch. I have used SRAdb and SRAdbV2 in the past, but these packages are no longer maintained ...
written 11 months ago by mark.ziemann1.3k
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Comment: C: How to get 1 top hit only for each query in blastx
... Duplicate question. You could try the suggested answer from a [previous post][1] [1]: https://www.biostars.org/p/131329/#131449 ...
written 11 months ago by mark.ziemann1.3k
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Comment: C: Macs2 output shows only single basepair peak instead of a section of DNA
... Could you give the version of MACS2 you are using and specify which output file you are referring to. There should be a narrowPeak.bed file present among the results. If you also provide the command you used to perform the analysis it will help us troubleshoot it for you. ...
written 11 months ago by mark.ziemann1.3k
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Comment: C: RNA seq with 2 biological replicates
... Here is another paper that might be interesting where they discuss RNA-seq without replicates [GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.][1] [1]: https://www.ncbi.nlm.nih.gov/pubmed/22923299 ...
written 11 months ago by mark.ziemann1.3k
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Answer: A: Location of Genes on Chromosome
... Gene location information can be found in the GTF or GFF files on the [Ensembl FTP site][1]. You just need to make sure that the version of the GTF/GFF file you use is the same as the annotation of the gene list you received. Older versions of Ensembl can be found at the [archive][2]. Here is the f ...
written 11 months ago by mark.ziemann1.3k

Latest awards to mark.ziemann

Appreciated 3 months ago, created a post with more than 5 votes. For A: JAVA and NGS
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Popular Question 7 months ago, created a question with more than 1,000 views. For Determine mutational profile from a BAM file?
Scholar 7 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Scholar 11 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Appreciated 23 months ago, created a post with more than 5 votes. For A: JAVA and NGS
Scholar 23 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Problem with creating GSEA rank file
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Determine mutational profile from a BAM file?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Digital Expression Explorer
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Scholar 3.2 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
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Scholar 3.6 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 4.7 years ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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