User: Ruolin Liu

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Ruolin Liu0
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Posts by Ruolin Liu

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Comment: C: How to deduplicate UMI with mapping shift ?
... Sorry, I know this thread has ended a while ago. But I am actually very curious about your statement "However, this enrichment disappears when expression levels are accounted for". I have checked your [notebook][1]. The final plot, correct me if I am wrong which I believe is the one account for expr ...
written 29 days ago by Ruolin Liu0
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Comment: C: True Positive rate of simulation
... Sorry. I should have put the references. ...
written 12 weeks ago by Ruolin Liu0
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True Positive rate of simulation
... In your landmark VG [Nat. Biotech paper][1], I am having a little bit of difficulty understanding ROC curve result of [Figure 2A][2]. As far as I think of comparing alignment, there is true and false but no positive/negative. If the alignment position matches the true position, it is true; otherwise ...
vg written 12 weeks ago by Ruolin Liu0
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PolyA reads in RNA-seq and how do aligners handle them?
... I've seen many polyA reads related question being asked in this forum many times but I still couldn't form a concrete answer for this. It seems to me that it is true that polyA reads do exist but some people say there are in low abundance. According to my simulation (I use FluxSimulator), there are ...
alignment rna-seq sequencing written 4.4 years ago by Ruolin Liu0 • updated 4.4 years ago by Brian Bushnell17k

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For PolyA reads in RNA-seq and how do aligners handle them?

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