User: rubic

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rubic210
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210
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United States
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1 month, 1 week ago
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6 years, 10 months ago
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Posts by rubic

<prev • 51 results • page 1 of 6 • next >
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Getting all the genomic coordinates where RNA-seq reads are split within a given genomic interval in a bam file
... Hi, I'm trying to improve the genomic annotation I have for a T-cell receptor gamma locus of a genome of intermediate annotation level, from bulk RNA-seq data. To briefly explain the situation, T-cells are born in the bone marrow and their T-cell receptor gamma locus has the germline genome struct ...
reads cigar splicing bam rna-seq written 7 weeks ago by rubic210 • updated 7 weeks ago by Pierre Lindenbaum134k
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GET Ensembl xrefs for multiple queries
... 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 ...
ensembl api httr written 6 months ago by rubic210 • updated 6 months ago by Ben_Ensembl1.6k
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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 20 months ago by rubic210
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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 20 months ago by rubic210
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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 20 months ago by rubic210 • updated 20 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 22 months ago by rubic210
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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 22 months ago by rubic210 • updated 22 months ago by Emily_Ensembl21k
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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 2.1 years ago by rubic210
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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 2.9 years ago by rubic210
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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 2.9 years ago by rubic210

Latest awards to rubic

Popular Question 14 months ago, created a question with more than 1,000 views. For Phasing X chromosome variants using shapeit2
Great Question 20 months ago, created a question with more than 5,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 20 months ago, created a question with more than 1,000 views. For Phasing X chromosome variants using shapeit2
Popular Question 22 months ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
Popular Question 22 months ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
Epic Question 2.1 years ago, created a question with more than 10,000 views. For GO enrichment analysis using R
Popular Question 2.1 years ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Phasing X chromosome variants using shapeit2
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Parsing BLAST pairwise output in R
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Piping a bam file to samtools calmd
Student 2.9 years ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Great Question 3.9 years ago, created a question with more than 5,000 views. For GO enrichment analysis using R
Popular Question 4.0 years ago, created a question with more than 1,000 views. For GO enrichment analysis using R
Student 4.1 years ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Getting: Error reading _plen[] array: 1776466139, 4294967292 with TopHat2/bowtie2

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