User: Fong Chun Chan

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Posts by Fong Chun Chan

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Comment: C: GenomicAlignments - Speeding up readGAlignmentPairs()
... Hi Herve, The R job is using 24g right now. I am operating on a machine with 128G so I don't think it is swapping as there isn't much running on it either. I am not using the use.names parameter. Fong On Mon, Jul 14, 2014 at 3:06 PM, Hervé Pagès wrote: > Hi Fong, > > > On 07/14/20 ...
written 3.3 years ago by Fong Chun Chan320
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Comment: C: GenomicAlignments - Speeding up readGAlignmentPairs()
... As promised, I put some of the run-time details for a particular bam file comparing readGAlignments vs. readGAlignmentsPairs. readGAlignmentPairs has been running for like over a week I believe and doesn't look like it will actually stop running...so I don't have any run-time of this function unfor ...
written 3.3 years ago by Fong Chun Chan320
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Comment: C: GenomicAlignments - Speeding up readGAlignmentPairs()
... Thanks for the reply. I understand what you mean about counting aligned pairs within a region and how that would give incorrect results. However, if I was purely interested in just getting all aligned read- pairs within the whole genomic space (no restriction to any region since this is what I need ...
written 3.4 years ago by Fong Chun Chan320
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Answer: A: GenomicAlignments - Speeding up readGAlignmentPairs()
... Hi Valerie, Thanks for the reply. I'll post some runtime as soon as it finishes running the readGAlignments and readGAlignmentPairs. Thanks for the tip on passing range(allExons) into the which param. There is only one issue in that if I wanted to then generate say RPKM values where I need to know ...
written 3.4 years ago by Fong Chun Chan320
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Comment: C: Using GenomicAlignments to get Exon-centric Counts
... Hi Valerie, Thanks for your reply. After re-reading that paired-end statement, I understand what you meant now and was definitely confused because I thought it was being treated as two single-end reads which would have defeated the purpose of using reading it in as a GAlignmentPairs object. Thanks ...
written 3.4 years ago by Fong Chun Chan320
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Using GenomicAlignments to get Exon-centric Counts
... Hi, Was wondering if anyone had any experience working with the GenomicAlignments R package when trying to retrieve per-exon count data? Specifically, whether these is rationale for using readGAlignmentsPairs() over readGAlignments() when using the summarizeOverlaps() function? From my understandin ...
written 3.4 years ago by Fong Chun Chan320 • updated 3.4 years ago by Valerie Obenchain ♦♦ 6.4k
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GenomicAlignments - Speeding up readGAlignmentPairs()
... Hi, I've been using the GenomicFeatures R package to read in some RNA-seq paired-end read data. While the readGAlignments() function reads in the bam file within a minute, I've noticed that the readGAlignmentPairs() function is extremely slow. This is even after restricting the space to just a sin ...
genomicfeatures written 3.4 years ago by Fong Chun Chan320
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Renaming the seqlevels in a transcript database from GenomicFeatures
... Hi, I am using the GenomicFeatures package to extract exons from a transcript database file. I am using the ensembl transcript database which has no chr, yet my bam files that I am working have the chr prefix. I was thinking one could append chr to the seqlevels in the transcript database like thi ...
genomicfeatures written 3.4 years ago by Fong Chun Chan320 • updated 3.4 years ago by Sonali Arora360
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VariantAnnotation R Package - Merging Two VCF files
... Hi, I wasn't able to find any thread about this, but is it possible to merge two vcf files in the VariantAnnotation R package? The two vcf files contain the exact same headers, columns, etc. Thanks, [[alternative HTML version deleted]] ...
variantannotation written 3.8 years ago by Fong Chun Chan320 • updated 3.8 years ago by Michael Lawrence9.8k
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Comment: C: VariantAnnotation - Accessing specific genomic ranges without needing a tabix fi
... Perfect thanks! On Wed, Feb 5, 2014 at 2:46 PM, Michael Lawrence wrote: > subsetByOverlaps(vcf, myRanges) > > > > On Wed, Feb 5, 2014 at 2:22 PM, Fong Chun Chan wrote: > >> Hi, >> >> I have question regarding accessing particular ranges of a VCF file that >& ...
written 3.8 years ago by Fong Chun Chan320

Latest awards to Fong Chun Chan

Popular Question 3.3 years ago, created a question with more than 1,000 views. For Renaming the seqlevels in a transcript database from GenomicFeatures
Student 3.3 years ago, asked a question with at least 3 up-votes. For Renaming the seqlevels in a transcript database from GenomicFeatures

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