Admin: Hervé Pagès
Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès
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Comment:
C: Biostrings install error
... Hi,
Are you using BiocManager::install() as recommended to install and update packages? It will spare you version mismatch headaches like the above.
H.
...
written 4 weeks ago by
Hervé Pagès ♦♦ 13k
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... This has been discussed and addressed on GitHub: https://github.com/Bioconductor/Biostrings/issues/15
H.
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written 5 weeks ago by
Hervé Pagès ♦♦ 13k
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Comment:
C: Modify Biostrings script
... You'll have to try it.
Also make sure to set no.init.codon to TRUE when calling translate() on sequences where the initiation codon has been removed or truncated. no.init.codon is a new argument to translate():
https://github.com/Bioconductor/Biostrings/commit/dcd915c21b96d4d981d4530f913ff910823 ...
written 5 weeks ago by
Hervé Pagès ♦♦ 13k
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Answer:
A: Modify Biostrings script
... Hi,
There is no need to start translating from the conserved site at the 3' end to stay in frame. When a read is truncated at the 5' end, all you need to do is trim 1 or 2 nucleotides on its 5' end to be in frame again. Or maybe you don't need to trim anything if the truncation preserved the frame. ...
written 5 weeks ago by
Hervé Pagès ♦♦ 13k
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... Maybe we could start by having a BiocViews term that we use to identify this type of package. Although this would make them "findable" only if you search/browse the right BioC version because our view trees are version specific: https://bioconductor.org/packages/release/BiocViews.html#___Software
P ...
written 5 weeks ago by
Hervé Pagès ♦♦ 13k
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... Hi,
Are you sure myGRangesObject is a GRanges object and not a GRangesList object?
Anyway you first need to come up with a GRanges (or GRangesList) object containing the genomic ranges of the sequences you want to pull out. For example, to grab the 1000 base pairs upstream of the ranges in myGRang ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
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... I might change a little bit the interface of the RleArray() constructor function though (e.g. replacing the chunksize argument with chunkdim). Other than that, as long as you don't serialize your RleMatrix instances and your code doesn't try to access directly the internals of these objects, any cha ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
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... Doesn't that limit to the total size of the matrix since it spans all columns?
Indeed. I should add that one of the original motivations for coming up with ChunkedRleArraySeed was exactly this limitation. I wanted to be able to load the 1.3 Million Brain Cell Dataset (https://bioconductor.org/packa ...
written 7 weeks ago by
Hervé Pagès ♦♦ 13k
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... Hi,
The exact internal representation of an RleArray object is still a work-in-progress and subject to change. The 2 current *RleArraySeed classes reflect the 2 experimentations I did so far with this. ChunkedRleArraySeed came after SolidRleArraySeed and improves on it by replacing a single Rle by ...
written 7 weeks ago by
Hervé Pagès ♦♦ 13k
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... I agree with Mike that this doesn't look like an issue related to Rsamtools. Please understand that It is very hard for the people watching this support site to help you if they cannot reproduce the error you're getting. So it would be of great help if you could provide a self-contained example that ...
written 7 weeks ago by
Hervé Pagès ♦♦ 13k
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For A: about setdiff() and meta-information in GRanges
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