User: rubic

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rubic180
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Posts by rubic

<prev • 46 results • page 1 of 5 • next >
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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 weeks 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 8 weeks ago by rubic180 • updated 7 weeks ago by Emily_Ensembl18k
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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 4 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 14 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 14 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 14 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 14 months ago by rubic180
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Does samtools view -b -h <input.bam> -L <input.bed> keep the original header?
... 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 ...
header samtools written 14 months ago by rubic180 • updated 14 months ago by d-cameron2.0k
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Number of sequenced positions from a BAM file
... 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? ...
bam samtools rna-seq written 2.2 years ago by rubic180 • updated 2.2 years ago by Devon Ryan90k
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Piping samtools merge to samtools calmd
... 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 ...
samtools pipe written 2.3 years ago by rubic180

Latest awards to rubic

Popular Question 6 weeks ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
Epic Question 4 months ago, created a question with more than 10,000 views. For GO enrichment analysis using R
Popular Question 4 months ago, created a question with more than 1,000 views. For At figure for an enrichment analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Phasing X chromosome variants using shapeit2
Popular Question 13 months ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 13 months ago, created a question with more than 1,000 views. For Parsing BLAST pairwise output in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 13 months ago, created a question with more than 1,000 views. For Piping a bam file to samtools calmd
Student 13 months ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Great Question 2.2 years ago, created a question with more than 5,000 views. For GO enrichment analysis using R
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GO enrichment analysis using R
Student 2.4 years ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 2.7 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 Efficiently extract alignments with NH:i:1 field
Popular Question 2.9 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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