User: rubic

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rubic180
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180
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United States
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2 days, 22 hours ago
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4 years, 10 months ago
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Posts by rubic

<prev • 44 results • page 1 of 5 • next >
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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 6 days 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 10 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 10 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 10 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 10 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 10 months ago by rubic180 • updated 10 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 22 months ago by rubic180 • updated 22 months ago by Devon Ryan88k
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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 23 months ago by rubic180
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Parsing BLAST pairwise output in R
... 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 ...
R parse blast written 2.1 years ago by rubic180
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Finding clusters of interacting proteins in a protein-protein interaction graph
... 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 ...
protein-protein-interaction enrichment ppi graph written 2.2 years ago by rubic180 • updated 2.2 years ago by Diwan560

Latest awards to rubic

Popular Question 9 months ago, created a question with more than 1,000 views. For Phasing X chromosome variants using shapeit2
Popular Question 9 months ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 9 months ago, created a question with more than 1,000 views. For Parsing BLAST pairwise output in R
Popular Question 9 months ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 9 months ago, created a question with more than 1,000 views. For Piping a bam file to samtools calmd
Student 9 months ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Great Question 22 months ago, created a question with more than 5,000 views. For GO enrichment analysis using R
Popular Question 23 months ago, created a question with more than 1,000 views. For GO enrichment analysis using R
Student 2.1 years ago, asked a question with at least 3 up-votes. For Create a UCSC chain file from a VCF
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Create a UCSC chain file from a VCF
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Efficiently extract alignments with NH:i:1 field
Popular Question 2.5 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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