User: rubic
rubic • 180
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Posts by rubic
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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 6 days 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 10 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 10 months ago by
rubic • 180
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... Think it was a bam header issue. Seems to work now. ...
written 10 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 10 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 22 months ago by
rubic • 180
• updated
22 months ago by
Devon Ryan ♦ 88k
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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 23 months ago by
rubic • 180
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... Hi,
Does anyone know of an R package that parses the pairwise format output of NCBI's blasp - which looks like this:
BLASTP 2.4.0+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gappe ...
written 2.1 years ago by
rubic • 180
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... Hi,
Given a protein-protein-interaction graph (e.g., from the string data base) and an outcome of a differential expression analysis (i.e., for each gene we have its log fold-change and the associated p-value between the treatment and control), is there a graph-based algorithm that can find subgrap ...
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