User: i.sudbery

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i.sudbery1.7k
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IanSudbery
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Posts by i.sudbery

<prev • 153 results • page 1 of 16 • next >
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Answer: A: Completely confused about terminology and what I'm actually analysing here
... 1. If is more or less impossible to know whether these contigs better represent genes or transcripts. I would be inclined to call the 'transfrags' (A TRANScripted FRAGment). This would of course be made easier if the organism in question does not have splicing. Then transcripts and genes are the sam ...
written 9 hours ago by i.sudbery1.7k
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Comment: C: Experience with dbGaP controlled access from outside the US?
... Reading that I'm personally quite relieved that not just any tom, richard or harry for a commercial organisation can get access to information that has only been consented by the patients that supplied it for a particular narrow purpose. ...
written 9 days ago by i.sudbery1.7k
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Comment: C: Experience with dbGaP controlled access from outside the US?
... Maybe I was lucky, but I applied on the 20th-ish of December and had access by the frist week on the new year, which I wouldn't say was too bad. ...
written 9 days ago by i.sudbery1.7k
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Answer: A: Experience with dbGaP controlled access from outside the US?
... Yes, we access lots of dbGap data from the UK. The first step is to apply for an eRA account. You will need the help of whomever is designated as the "signing officier" at your university. If your university does not have one, then your university will first need to register. See here: https://era. ...
written 9 days ago by i.sudbery1.7k
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Comment: C: Filtering out low expressed genes in RNA-Seq data
... I guess the worry here is that lowly expressed genes have more noise and thus will screw up the correlations. I'm not sure anyone has every really considered this question, nor can I think of a principled approach. The key thing with correlations is probably to get rid of the zeros. Too many zeros ...
written 7 weeks ago by i.sudbery1.7k
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Comment: C: Uniquely mapped in Human
... See the answer below. I guess those samples with <5% are almost certainly a dead loss, however you could look at the counts of reads that map to genes. I'd guess you'd want at least around 10M to use a sample. ...
written 7 weeks ago by i.sudbery1.7k
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Answer: A: Filtering out low expressed genes in RNA-Seq data
... I depends on what your downstream analysis is. If your aim is to filter low expressed genes to increase power in a differential expression analysis, I recommend reading [Data-driven hypothesis weighting increases detection power in genome-scale multiple testing][1] If you want to divide genes into ...
written 8 weeks ago by i.sudbery1.7k
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Comment: C: Uniquely mapped in Human
... 5% is VERY low for 2x100bp reads. I would normally expect a minimum of 70%, and I guess we average above 90% with STAR. If you look at your STAR output, you'll see that your problem is that 90% of reads map to multiple loci. If this is standard RNA-seq, my first guess would be that you have fa ...
written 8 weeks ago by i.sudbery1.7k
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Answer: A: should I merge fastq files for different lanes before do QC?
... In general we only merge after mapping. There are several reasons for this: Your QC might pick up a lane specific problem: i.e. 3 of your 4 lanes might have worked fine, but one might have failed. Even if your QC doesn't pick up anything, the mapping might (after all % of uniquely mapped reads is t ...
written 8 weeks ago by i.sudbery1.7k
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Comment: C: Download SAM/BAM files from SRA takes ages!!!
... I never thought of that.... what a great idea! ...
written 8 weeks ago by i.sudbery1.7k

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