User: predeus
predeus • 1.1k
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Posts by predeus
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... Good call - like I said, "unless something has changed"!
I agree, the results should be very comparable. ...
written 1 day ago by
predeus • 1.1k
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... Unless something has changed dramatically, you should use Picard and not samtools to mark duplicates in an aligned file. Even Heng Li (the author of samtools) said that he does not recommend using samtools markdup. The topic was discussed quite a lot, for example, here: http://seqanswers.com/forums/ ...
written 2 days ago by
predeus • 1.1k
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... You can try Ugene - it's quite user-friendly and should do multiple sequence alignment and visualization.
http://ugene.net/ ...
written 2 days ago by
predeus • 1.1k
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... So there's this tool that basically is used for interactive expression analysis: http://genome.ifmo.ru/phantasus-dev/
But you can use it to do heatmap-based visualization of nearly anything.
Cluster your table using k-means and then sort by cluster. You should get a pretty good idea of feature ov ...
written 2 days ago by
predeus • 1.1k
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... If you want to circularize the genome, I'd assume you are assembling a bacterial genome?
If you have pacbio only, best assembler right now is Flye - it's very accurate, does not mess up the circularization, and generates quite nicely finished contigs
If you have pacbio + illumina, Unicycler does ...
written 28 days ago by
predeus • 1.1k
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Comment:
C: Batch effect correction
... Yes, I meant you incorporate your "batch" variable into Deseq2 formula, and use NON-batch corrected data. Authors of comBat acknowledged that it might be over-correcting it that way. ...
written 6 weeks ago by
predeus • 1.1k
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... why do you want to do it manually? Most modern quantification programs (featureCounts, rsem, kallisto, salmon) will do it for you.
It's more complicated than just transcript length (and what is **mean** transcript length?) - the formula is
> transcript length - mean fragment length + 1
(and ...
written 7 weeks ago by
predeus • 1.1k
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... I'll go on a limb here and say that there is no clear benefit of switching from hg19 to hg38 for most purposes.
So hg19 will become obsolete same time as hg38, when using graph-based genome reference will become feasible. ...
written 7 weeks ago by
predeus • 1.1k
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... Depends on why do you need the visualization, right? Visualization can be done to explore the data, or to make a point in the publication etc
If you want to explore the data, you can also try and specify for yourself, what exactly you want to find out - specific genes? Certain pathways? all this ma ...
written 7 weeks ago by
predeus • 1.1k
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... I would look carefully into how you associate a particular feature with a gene name
e.g. some genes are very long
but, to answer your question, I think you are correct to assume that odds ratio would show the strength of association. ...
written 7 weeks ago by
predeus • 1.1k
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