User: rubic
rubic • 180
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Posts by rubic
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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 6 months ago by
rubic • 180
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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 6 months ago by
rubic • 180
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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 7 months ago by
rubic • 180
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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 7 months ago by
rubic • 180
• updated
7 months ago by
Emily_Ensembl ♦ 20k
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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 10 months ago by
rubic • 180
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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 20 months ago by
rubic • 180
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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 20 months ago by
rubic • 180
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... Think it was a bam header issue. Seems to work now. ...
written 20 months ago by
rubic • 180
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... Hi,
I have mouse `RNA-seq` data (`single-end` stranded - reverse strand) which I `STAR` mapped against `mm10` with `gencode.vM12.primary_assembly.annotation` `GTF`, where I ran `STAR` in a mode that also generates a `bam` file of the reads mapping to the `transcriptome`.
For my purpose I'd like to ...
written 20 months ago by
rubic • 180
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