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Recent Replies
Comment: Limma model gives weird results
by
leranwangcs
▴
150
thanks!
There was a typo in the model and it was supposed to be:
model.design <- model.matrix(~ Dx.Status + Country + month + solid_f…
Comment: Is vg toolkit suitable for haplotype calling?
by
Pau
•
0
Just to be more explicit: I am working with a polyploid monoexonic gene whose boundaries are well annotated. I have many cDNA ONT reads (fu…
Answer: Unable to find mitochondrial genes in latest rat genome(GRCr8)
by
GenoMax
150k
It appears that the mitochondrial genome has not made it to the `RefSeq` version of GRCr8. It is present in GenBank version though: https:/…
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
Nerelys
•
0
Yes, I will consider that also. Thanks a lot!
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
GenoMax
150k
> as I do not have sufficient resources to generate the index myself.
If that is the case you may also run into issues with alignments. ST…
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
dsull
★
7.4k
Darn it lol! Think you beat me by a second!
Answer: Pre-Made STAR Index for mm10 Mouse Genome
by
dsull
★
7.4k
Found this online :)
http://refgenomes.databio.org/v3/assets/splash/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/star_index?tag=defa…
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
Of course! Oh, the parameter is --d-list. By default, in `kb ref`, --d-list is set to whatever FASTA you supply to `kb ref` but you can dis…
Comment: STAR vs. Kallisto
by
gogeni5529
▴
60
thanks @delaneyksull for the comprehensive responses both in the answer as well as in the comments. I appreciate the time.
A comment to y…
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…
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