User: aquaq

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aquaq30
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3 years, 10 months ago
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Posts by aquaq

<prev • 29 results • page 2 of 3 • next >
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Comment: C: How to run sleuth in single run mode?
... You are right, I have misread it. Thank you! ...
written 23 months ago by aquaq30
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How to run sleuth in single run mode?
... Hi! I have run kallisto on RNA-Seq data from SRA. Unfortunately, it does not have any replicates. After kallisto, I try to run sleuth with recommended commands (https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html). However, sleuth_fit gives an error the exact same as described i ...
sleuth kallisto rna-seq written 23 months ago by aquaq30
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Rna-seq: How to normalize them with biological replicates to get change ratio?
... We have a cell line with certain plasmids added. The initial sample was split into three subsamples, plus it was sequenced once. The three subsamples were grown differently, then each sequenced once (of course the four library was pooled begore sequencing with their respective barcodes added). The s ...
rna-seq written 2.8 years ago by aquaq30
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Comment: C: Why do they use ratios for differential expression analysis?
... Thanks. I was thinking on microarray and realozed that with flurescency, it might be ratio scale. However, I've read that RNA-Seq measure counts relative to the number of all reads, and absolute quantification would be possible by adding controls (spikes). ...
written 2.8 years ago by aquaq30
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Why do they use ratios for differential expression analysis?
... I was interested in differential expression and started to read related materials. They all state that both RNA-seq and microarray data gives relative abundances (I understand that both can be absolute with some reference). As far as I know, this means interval scale instead of ratio scale. Then, th ...
differential expression statistics written 2.8 years ago by aquaq30
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Comment: C: What makes a good bionformatics prediction service?
... Thank you! I will make a mental not to myself - finding the right expression may worth a lot more than dozens of words. Just to enhance other's "forum experience". ...
written 3.0 years ago by aquaq30
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Comment: C: What makes a good bionformatics prediction service?
... My question is **not about the performance** of the predictions but rather how to make their usage user-friendly by setting up webpages that are easily usable, stable and provide all the features that would help the work of a user (both other bioinformaticians and experimentalist researchers). As ...
written 3.0 years ago by aquaq30
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Comment: C: What makes a good protein properties prediction service?
... I'm sorry, I have to revert it, I have already added 'bioinformatics'. Protein properties were only examples for a question above, I am interested in all kinds of bioinformatics prediction services in general. ...
written 3.0 years ago by aquaq30
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Comment: C: What makes a good prediction server?
... Thanks for the feedback, I will try to make myself clearer: bioinformatics researchers often make prediction services for protein structure/function/subcellular localizations/interactions/PTMs/glycolization/disorder/transmembrane topology whatever (same things apply for DNA/RNA predictions but I am ...
written 3.0 years ago by aquaq30
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Forum: What makes a good bionformatics prediction service from the point of user experience?
... Most of us tried to use one or more bioinformatics prediction services. We probably all have came across good and bad ones. How do you decide which one to use? What features make it more/less probable that you would stick to one? Let's assume that the underlying algorithms have the same performance. ...
server good forum prediction service written 3.0 years ago by aquaq30

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For How to merge paired-end reads from sam files?

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