User: rubic

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rubic180
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Posts by rubic

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Get Ensembl mapping between the chromosome and scaffold names
... 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 rubic180
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Comment: C: Get Ensembl mapping between the chromosome and scaffold names
... 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 rubic180
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Get Ensembl mapping between the chromosome and scaffold names
... 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: ...
ensembl scaffold assembly chromosome written 6 months ago by rubic180 • updated 6 months ago by crisime190
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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 rubic180
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AGP files in Ensembl
... 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 ...
assembly agp ensembl written 7 months ago by rubic180 • updated 7 months ago by Emily_Ensembl20k
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Parse sim4 output alignment format
... 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 ...
sim4 parse pairwise alignment written 10 months ago by rubic180
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Getting transcriptomic coordinates for CDS exons from a GTF
... 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`? ...
gtf bed written 20 months ago by rubic180
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Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
... 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 rubic180
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Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
... Think it was a bam header issue. Seems to work now. ...
written 20 months ago by rubic180
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Running salmon after subsetting the bam to transcripts annotated as protein coding in the GTF
... 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 ...
gtf salmon samtools gencode written 20 months ago by rubic180

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Popular Question 7 months ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
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Epic Question 10 months ago, created a question with more than 10,000 views. For GO enrichment analysis using R
Popular Question 10 months ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
Popular Question 19 months ago, created a question with more than 1,000 views. For Phasing X chromosome variants using shapeit2
Popular Question 19 months ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 19 months ago, created a question with more than 1,000 views. For Parsing BLAST pairwise output in R
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Student 19 months ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Great Question 2.7 years ago, created a question with more than 5,000 views. For GO enrichment analysis using R
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
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