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Recent Replies
Comment: Is vg toolkit suitable for haplotype calling?
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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!
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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…
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Darn it lol! Think you beat me by a second!
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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.
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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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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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GeneSCF may be an option: https://github.com/genescf/GeneSCF?tab=readme-ov-file#Step-by-step-instructions
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