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Recent Replies
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
Also, this isn't arguing for/against kallisto. You're mentioning situations about ALIGNMENT issues; this is a QUANTIFICATION issue.
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
A ton of benchmarking (across many papers) has already been done to show which tools perform best when. The literature has a ton of evidenc…
Comment: The volcano plot shows data with an arm-shaped enrichment.
by
ATpoint
87k
Usually odd shapes in these sorts of plots come from insufficient prefiltering. Here, in your `keep` all you do is to make sure that the ge…
Comment: STAR vs. Kallisto
by
ATpoint
87k
Unless you comprehensively show that one tool performs globally better and reveals more meaningful biology than the other the choice is in …
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
After re-reading this, I'm going to push back against this answer a bit. In this case, it's 100% clear that pseudoalignment is producing th…
Comment: Is there a tool to obtain GO terms for thousands of genes at once?
by
GenoMax
150k
GeneSCF may be an option: https://github.com/genescf/GeneSCF?tab=readme-ov-file#Step-by-step-instructions
Please be aware that use of KEGG…
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
On the contrary, I think the right approach is to test each tool and see where the difference arises :) -- papers would be much more inform…
Comment: STAR vs. Kallisto
by
ATpoint
87k
I use salmon-tximport/lengthScaledTPM-limma most of the time but other combinations work fine as well.
Answer: STAR vs. Kallisto
by
dsull
★
7.4k
I use both STAR and kallisto extensively (and I help develop the latter).
kallisto is nice when you care about asking the question "does…
Comment: STAR vs. Kallisto
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Thanks for the explanation. Do you use salmon after STAR and followed by DESeq2 to do differential expression analysis (using tximport)? Or…
Answer: STAR vs. Kallisto
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Basically, choice of tools is always a bit of arbitrary given that both tools are established and well recognized.
STAR does splice-aware …
Comment: Is there a tool to obtain GO terms for thousands of genes at once?
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Ana
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Is there a tool to do this but with KEGG pathways instead? Thanks.
Answer: Phylogenetic Comparative Methods in R (12–16 May, Online)
by
Meeru
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Thanks for the heads-up! Sounds like a great opportunity for anyone working with phylogenies and R. Definitely useful for evolutionary rese…
Comment: Is vg toolkit suitable for haplotype calling?
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The read alignment is a path through the graph, so in that sense, I think the read alignment might be the path you are looking for. For dow…
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