User: i.sudbery

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i.sudbery1.8k
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IanSudbery
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Posts by i.sudbery

<prev • 176 results • page 1 of 18 • next >
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Comment: C: HISAT index incomplete even with HUGE RAM
... Two things about your SGE spec there: 1) You are asking for 64GB *per core* and 8 cores. This means you are asking for 512GB. However, 2) you are also asking for this as virtual memory rather than physical memory, and HISAT can't use virtual memory. Couple of things you might like to try: addi ...
written 2 days ago by i.sudbery1.8k
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Comment: C: HISAT index incomplete even with HUGE RAM
... On every SGE system I have worked on specifying h_vmem does not limit memory usage for the task, rather it tells the queue controller not to kill the job for using too much memory. That is if you specify `h_vmem=24GB` using 25GB will not result in an out of memory error (as long as the memory exist ...
written 2 days ago by i.sudbery1.8k
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Job: Mixed wet/dry Postdoctoral Reserach Assoicate - University of Sheffield
... The laboratory of Dr. Ian Sudbery, in collaboration with Prof. Stuart Wilson, seeks a Research Associate to work on a mixed molecular biology/bioinformatics project examining the role of splicing in regulating the stability and non-coding sequence content of transcripts in cancer and normal biology. ...
splicing cancer rna job mirna written 8 days ago by i.sudbery1.8k
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Comment: C: Analyzing RNA-seq without replicates
... Yes. The fold changes for each patient will still be indicative of what is happening for that patient, but its difficult to know how accurate they are. ...
written 9 days ago by i.sudbery1.8k
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Answer: A: Analyzing RNA-seq without replicates
... Do not analyse the patients separately. In that design you have not replicates. And even if you could analyse them without replicates, looking for overlaps is a terrible way of finding which effects are significant - it relies on the arbitrary thresholds you have choosen to use to call significance ...
written 10 days ago by i.sudbery1.8k
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... The choice of pseudo-count is not clear, and there are often threads on Twitter debating the issue. The rlog transformation from DESeq takes a principled approach to finding a suitable psuedo-count from the data. ...
written 20 days ago by i.sudbery1.8k
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... You may wish to look into [Schurch et al, 2016][1] (and related papers) out of Geoff Barton'l lab who did a two condition experiment with 47 replicates in each condition in order to benchmark various assumptions and methods for RNAseq. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878611/ ...
written 5 weeks ago by i.sudbery1.8k
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... > It's that only genes with the same expression have the same variance You were right the first time with similar, rather than the same. What the empirical bayes says is not that all genes have the same variance, but that in the absence of any data, if you guessed the average variance for genes ...
written 5 weeks ago by i.sudbery1.8k
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... The standard empirical bayes methodology would be to assume that all genes have the same variance unless there was evidence to the contrary and use the all replicates of all genes to obtain a best estimate of this prior equal variance and then apply evidence from each sample to shift each gene away ...
written 5 weeks ago by i.sudbery1.8k
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Comment: C: What is the number of reads would you recommend to analyze lncRNAs without loss
... Using any standard RNA-seq protocol you can't analyse miRNAs and mRNA/lncRNA in the library prep. Almost all library prep protcols involve a size selection. miRNAs are around 22nt and require specialist methods to prepare libraries from them. lncRNAs/mRNAs usually involve selecting fragment sizes in ...
written 5 weeks ago by i.sudbery1.8k

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Scholar 9 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 10 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 10 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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