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Mark Ziemann
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Get the newest Reactome gene sets for pathway analysis
For first-pass pathway analysis I find Reactome to be the most useful database of gene sets for biologists to understand. For a long time I have been using Reactome gene sets as deposited to the GSEA/MSigDB website. Recently a colleague pointed me to the ge...
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Publishing datasets on the dat network
As I mentioned in an earlier post , Dat is a new data sharing tool that uses concepts of bittorrent and git to enable peer-to-peer sharing of versioned data. This is cool for sharing datasets that change over time, because when you sync the dataset, only th...
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Has RNA-seq overtaken microarrays?
We know RNA-seq has a number of advantages over array based analyses, but is RNA-seq taking over in terms of number of datasets published? I got curious and thought I'd investigate with some PubMed searches. I searched for "RNA-seq" and "microarray" and dow...
Has RNA-seq overtaken microarrays?
Has RNA-seq overtaken microarrays?
genomespot.blogspot.com
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Share and backup data sets with Dat
If you work in genomics, you'll know that sharing large data sets is hard. For instance our group has shared data with our collaborators a number of ways: DVDs, hard drives and flash drives FTP Hightail Google Drive links Amazon links SCP/PSCP rsync But non...
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convert a human gmt file to mouse for GSEA
convert a human gmt file to mouse for GSEA
crazyhottommy.blogspot.com.au
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update on DEE2 project for Jan 2018
Today I'd like to share some updates on the DEE2 project, which I wrote about  in an earlier post . The  project code can be viewed on github here . Pipeline and images As the pipeline was recently finalised. I was able to roll out the working docker image....
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Update on the DEE project Dec 2017
Back in 2015, our group described DEE, a user friendly repository of uniformly processed RNA-seq data, which I covered in detail in a previous post . Ours was the first such repository that wasn't limited to human or mouse and included sequencing data from ...
Update on the DEE project Dec 2017
Update on the DEE project Dec 2017
genomespot.blogspot.com
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Diagnosing PCR duplicates from cluster duplicates
NovaSeq, HiSeqX and HiSeq4000 Illumina sequencers have patterned flowcells which have a different chemistry as compared to random clustered flowcell systems (Hiseq2500 & MiSeq) which is known to cause duplicates during the clustering process. For some backg...
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Considerations in performing whole human genome bisulfite sequencing on the Illumina NovaSeq system
Today at the NGS workshop at WEHI, Melbourne, I presented some findings related a pilot study of 12 methylomes studied with whole genome bisulfite sequencing. Two of those libraries were also sequenced on the HiSeq4000 platform to similar depth so there wer...
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