User: rubic
rubic • 190
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Posts by rubic
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... Hi,
I'm using Ensembl's [rest][1] to obtain xrefs. The example shows how to do this.(I'm using the `R` option) for a single Ensembl gene ID query, but I'd like to obtain xrefs for all the gene IDs in the GTF.
Is there a way to use the `httr` `GET` function that in the example with multiple querie ...
written 12 hours ago by
rubic • 190
• updated
6 hours ago by
Ben_Ensembl • 1.5k
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... No, the scaffolds I see in the GTF of the latest marmoset genome assembly - Callithrix_jacchus.ASM275486v1.95.gtf, are: NTIC01000001.1, NTIC01000002.1, NTIC01001061.1, ..
The [assembly information page][1] also mentions that this genome is in scaffolds. That page also refers to its NCBI assembly ac ...
written 14 months ago by
rubic • 190
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... Thanks @Emily_Ensembl. Do you mean specifically for the Marmoset genome?
[This Ensembl page][1] says that the genome assembly is at the scaffold level.
[1]: https://uswest.ensembl.org/Callithrix_jacchus/Info/Annotation ...
written 14 months ago by
rubic • 190
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... Hi,
I'm trying to follow up on [this post][1], for mapping between Ensembl's scaffold names and NCBI's assembly scaffold/chromosome names.
Like in the previous post, as an example, I'm trying to that for the Marmoset genome.
I'm a newbie to Ensembl's API, so this is as much as tried so far:
...
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Comment:
C: AGP files in Ensembl
... Thanks a lot @Emily_Ensembl.
Can that table somehow be retrieved using `Bioconductor`'s `biomaRt`?
Or is only retrievable using MySQL? ...
written 15 months ago by
rubic • 190
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... Hi,
Does anyone know where can AGP files be downloaded from Ensembl's website?
I'm using Ensembl's annotations for several genomes but can only find AGP files for them on NCBI and unfortunately for several of the genomes Ensembl's scaffold names do not match those of NCBI's.
For example the marmo ...
written 16 months ago by
rubic • 190
• updated
15 months ago by
Emily_Ensembl ♦ 21k
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... Hi,
This is somewhat redundant with [this post][1], which has not been fully answered.
I'm using Webb Miller's [sim4][2] aligner, which output (specifying A=1 in the arguments) looks like this:
seq1 = /data/seq1.fa, 1095 bp
seq2 = /data/seq2.fa (chrA:23544043-25452600), 1908558 bp
...
written 18 months ago by
rubic • 190
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... Hi,
Is there an `R` `package`/`function` that given a `GTF` file (or in a `data.frame`) can return a `data.frame` where each row is a `CDS` `exon` and its start and end coordinates relative to the `spliced` `transcript`?
...
written 2.3 years ago by
rubic • 190
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... I had an error in how I edited the bam's error which produced this problem so I don't think it's worth posting. ...
written 2.3 years ago by
rubic • 190
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... Think it was a bam header issue. Seems to work now. ...
written 2.3 years ago by
rubic • 190
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