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Recent Replies
Comment: What does canonical transcript mean in the context of VEP
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> Does that mean the fully functional gene most folks think of when thinking of their favorite gene?
That ... doesn't make much sense. Did…
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https://www.ensembl.org/info/genome/genebuild/canonical.html
> The Ensembl Canonical transcript is a single, representative transcript ide…
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In an unsorted BAM file, reads can be in any random order. In a co-ordinate sorted BAM file, reads are in the order in which they map to th…
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how does it correspond to 27.2 ? or these are the other proteins ?
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Normalize them first using `vt normalize` or `bcftools norm` - they need to be in left-aligned parsimonious representation before you can d…
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You need to perform batch effect removal for these. Seurat has its integration protocol, and if you use scverse on Python, the usual choice…
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I added the link for NCBI "book" since DIAMOND seems to follow the format/reporting structure for blast+ results. While the numbers shown i…
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`PASS` + `filter_name` is `filter_name`, not `PASS,filter_name`. PASS means the locus hit no filter. You'll never see a `PASS,<something>`.…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
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Alexander
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Thank you for the reply ! I got seems to be even more puzzled here - we see "identities" 95% while in the example "pident" is 27.2 - so …
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Thanks a lot for the explanation!
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Thank you !
@buchfink would you be so kind to comment ?
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As the previous poster said we’re not sure what you’re looking for, but the basic data are available at the NCBI ftp site (linked from the …
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Thank you both for your answers @masklin @ram !
For anyone facing the same problem, I followed Ram's suggestions and it worked beautifully…
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I need a phylogenetic tree for those 5 genomes
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