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Recent Replies
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GenoMax
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Showing plots may lead to answers/comments. A picture can be worth more than a given number of words.
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> I’d like: • One row per gene • One column with the gene name/ID • Another column with Wormbase's automated short description
You can go…
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Thanks for pointing it out. I appreciate the help.
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thanks!
There was a typo in the model and it was supposed to be:
model.design <- model.matrix(~ Dx.Status + Country + month + solid_f…
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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…
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It appears that the mitochondrial genome has not made it to the `RefSeq` version of GRCr8. It is present in GenBank version though: https:/…
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Yes, I will consider that also. Thanks a lot!
Comment: Pre-Made STAR Index for mm10 Mouse Genome
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> 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
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Darn it lol! Think you beat me by a second!
Answer: Pre-Made STAR Index for mm10 Mouse Genome
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Found this online :)
http://refgenomes.databio.org/v3/assets/splash/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/star_index?tag=defa…
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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…
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thanks @delaneyksull for the comprehensive responses both in the answer as well as in the comments. I appreciate the time.
A comment to y…
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Also, this isn't arguing for/against kallisto. You're mentioning situations about ALIGNMENT issues; this is a QUANTIFICATION issue.
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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…
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