User: rubic
rubic • 180
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Posts by rubic
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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 weeks 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 8 weeks ago by
rubic • 180
• updated
7 weeks ago by
Emily_Ensembl ♦ 18k
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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 4 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 14 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 14 months ago by
rubic • 180
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... Think it was a bam header issue. Seems to work now. ...
written 14 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 14 months ago by
rubic • 180
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... Simple question
Seems like the command:
samtools view -b -h -L
for subsetting the `bam` file to keep only those reads intersecting the `seqnames` and their regions in `input.bed` is retaining the original `header` in the output `bam` file, including those `seqnames` not present in `input.be ...
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... Hi,
Is there a samtools or other tool command that given a bam (and/or indexed bam) file will report the number of sites sequenced?
...
written 2.2 years ago by
rubic • 180
• updated
2.2 years ago by
Devon Ryan ♦ 90k
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... Hi,
Suppose I have 2 bam files: `left.bam` and `right.bam` that I want to merge and then `pipe` the outputed merged file to `samtools calmd` with a `ref.fasta` file. Will the appropriate command be:
samtools -n - left.bam right.bam | samtools calmd -b - ref.fasta
...
written 2.3 years ago by
rubic • 180
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