User: Taylor, Sean D

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Posts by Taylor, Sean D

<prev • 24 results • page 1 of 3 • next >
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Comment: C: variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
... Valerie, I am excited about these changes and can't wait to use them. For clarification, to use genetic.code, I would pass in an argument like this: predictCoding(..., genetic.code=mycode) where 'mycode' is a named vector of same format as GENETIC_CODE used in translate(). I haven't been using ...
written 5.7 years ago by Taylor, Sean D250
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Comment: C: Problem with BAM header in GAlignments
... Thanks Martin. For what its worth, using asBam() did not work: > asBam(bamfile, 'test.bam', indexDestination=TRUE) Error in value[[3L]](cond) : 'asBam' SAM/BAM header missing or empty file: '03-192B3_lung.sort.nodup.bam.realigned.bam' SAM file: '03-192B3_lung.sort.nodup.bam.realigned.bam' In ...
written 5.8 years ago by Taylor, Sean D250
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Comment: C: Problem with BAM header in GAlignments
... The thought did occur to me that these might be SAM format, but its odd because the information beyond the header appears to be binary. The files also came with accompanying .bai index files as well. I have never had cause to carefully examine the header, so I didn't know what to expect. I take it t ...
written 5.8 years ago by Taylor, Sean D250
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Answer: A: Problem with BAM header in GAlignments
... I apologize if this is a repeat, but I'm not sure this went through the first time I tried it. I have received some BAM files from a colleague that were produced from an Illumina HiSeq instrument. When I try to read them as a GAlignments object, I get the following error: > bamfile<-'03-192B3_ ...
written 5.8 years ago by Taylor, Sean D250
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Problem with BAM header in GAlignments
... I have received some BAM files from a colleague that were produced from an Illumina HiSeq instrument. When I try to read them as a GAlignments object, I get the following error: > bamfile<-'03-192B3_lung.sort.nodup.bam.realigned.bam' > gal<-readGAlignments(bamfile) Error in value[[3L]](c ...
cancer written 5.8 years ago by Taylor, Sean D250 • updated 5.8 years ago by Martin Morgan ♦♦ 23k
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Comment: C: Phred encoding
... Martin and others, I'm following a methodology in a paper for some NGS sequence analysis (He et al. Nature, 2010, vol 464, p610). In this paper, they apply three quality filters to the reads (36 bp reads from Genome Analyser II instrument): 1. all 36 bases in a read are required to have a Phred sco ...
written 6.2 years ago by Taylor, Sean D250
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Comment: C: Phred encoding
... Thanks for the response Vincent. I'm afraid I still don't understand what as.raw() is doing differently. Did part of your reply get cut off? After consulting ?as.raw() I still would have expected the answer that as.numeric() is generating (based on my limited understanding). From: Vincent Carey [ma ...
written 6.2 years ago by Taylor, Sean D250
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Phred encoding
... Hi, I'm trying to quality filter my NGS reads and want to filter out reads that have bases below a quality threshold (say 23 for instance, using Illumina MiSeq with an offset of 33). Can anyone tell me why the results of the two functions as.raw() and as.numeric() give different results? qual<- ...
written 6.2 years ago by Taylor, Sean D250 • updated 6.2 years ago by Vincent J. Carey, Jr.6.3k
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Answer: A: DNAStringSetList can't coerce a list?
... Nevermind. I restarted my R session and that seems to have helped. From: Taylor, Sean D Sent: Monday, August 05, 2013 4:59 PM To: bioconductor@r-project.org Cc: Pages, Herve (hpages@fhcrc.org) Subject: RE: DNAStringSetList can't coerce a list? Sorry, here is my sessionInfo() > sessionInfo() R v ...
written 6.2 years ago by Taylor, Sean D250
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Answer: A: DNAStringSetList can't coerce a list?
... Sorry, here is my sessionInfo() > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPE ...
written 6.2 years ago by Taylor, Sean D250

Latest awards to Taylor, Sean D

Popular Question 5.7 years ago, created a question with more than 1,000 views. For Problem with BAM header in GAlignments
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Trimming of partial adaptor sequences

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