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:
23 hours ago
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5 years, 7 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 • 158 results • page 1 of 16 • next >
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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 2 days 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 2 days 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 7 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 7 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 7 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 7 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 7 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 7 months ago by mark.ziemann1.3k
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Comment: C: find a correct gene symbol for lncRNA
... Is this an Ensembl transcript ID? If so, you can use [Ensembl BioMart][1] to obtain tables that relate transcript and gene IDs. [1]: https://www.ensembl.org/biomart/martview ...
written 7 months ago by mark.ziemann1.3k
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Comment: C: /bin/bash/ command not found
... Apologies - I will edit ...
written 7 months ago by mark.ziemann1.3k

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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: tRNA expression analysis from RNA-Seq
Popular Question 3 months ago, created a question with more than 1,000 views. For Determine mutational profile from a BAM file?
Scholar 3 months ago, created an answer that has been accepted. For A: Get CDS from WGS fasta OR download just CDS
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