User: Lakshmanan Iyer

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Posts by Lakshmanan Iyer

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BSgenome.Hsapiens.UCSC.hg19 Sequence missing
... Hi I downloaded the latest bsgenome...hg19. How many of the chromosomes have "N" as sequence. however, chrM and others have regular letters. Am I missing something here? more information below > library ("BSgenome.Hsapiens.UCSC.hg19") > genome <- BSgenome.Hsapiens.UCSC.hg19 > genome ...
bsgenome hg19 written 2.1 years ago by Lakshmanan Iyer250 • updated 2.1 years ago by Martin Morgan ♦♦ 20k
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Answer: A: Creat PWM from Alignment with Gaps
... Thanks Herve That work around worked.... -best -Lax On Tue, Oct 1, 2013 at 2:53 PM, Hervé Pagès wrote: > Hi Lax, > > > On 09/25/2013 09:52 AM, Lakshmanan Iyer wrote: > >> In Bioconductor, Is it possible to create a PWM from DNA sequence >> alignment >> with gaps ...
written 4.0 years ago by Lakshmanan Iyer250
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Creat PWM from Alignment with Gaps
... In Bioconductor, Is it possible to create a PWM from DNA sequence alignment with gaps to be used to scan sequences? When I try it as suggested in "Biostrings" it gives the following error: > pwm <- PWM(pfm) Error in .normargPfm(x) : invalid PFM 'x': IUPAC ambiguity letters are represented ...
written 4.1 years ago by Lakshmanan Iyer250
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Comment: C: readGapppedAlignmentpairs questions
... Hi Herve, Thanks! I have a server with 96GB of memory, so now swap issues. I just downloaded and installed the dev branch of bioconductor on my server so that I have the latest Rsamtools to work with. We are using "Star" to map the reads and it looks like it produces many multi-mapped reads and the ...
written 5.3 years ago by Lakshmanan Iyer250
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readGapppedAlignmentpairs questions
... Hi My apologies for multiple posting if it happens-- I sent the last mails from other accounts which may not be registered with Bioc-list -Lax Two questions: 1. Is readGapppedAlignmentPairs - the most efficient way to read a paired-end bam file with mulit-mapped reads? I am asking as it takes an en ...
coverage process written 5.3 years ago by Lakshmanan Iyer250 • updated 5.3 years ago by Wei Shi2.6k
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Coverage on GappedAlignmentPairs
... Hi How does one work with coverage on GappedAlignmentPairs in the context of RNASeq? The simplest way is to consider each left and right read as separate - essentially loose the "paired" information and calculate coverage. However, if both the left and right pair reads fall within a feature of int ...
coverage written 5.3 years ago by Lakshmanan Iyer250
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Comment: C: Coverage Question: GenomicRanges
... You are right. From the picture attached, I could see that only the first read is on + strand, the other three are - strand and are being ignored. Let me rerun and see Best Lax Sent from my iPhone On Mar 9, 2012, at 1:05 PM, Michael Lawrence wrote: > One possibility is that you need to use i ...
written 5.6 years ago by Lakshmanan Iyer250
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Coverage Question: GenomicRanges
... I am calculating the coverage on a subset of a gapped aliment that obtained using "subsetByOverlaps" between a "GappedAlignments" and a "GRanges" object #> class (Dendaligns) #[1] "GappedAlignments" #attr(,"package") #[1] "GenomicRanges" #> class (p3UTRsChr) #[1] "GRanges" #attr(,"package") #[ ...
coverage convert written 5.6 years ago by Lakshmanan Iyer250 • updated 5.6 years ago by Michael Lawrence9.6k
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Faster way to apply a function than endoapply on 40K GrangesList
... Hi, I am trying to add 10K to the end of the intervals in a GRangesList object using endoapply and flank using the comand: p3UTRs10K <- endoapply(p3UTRs,function (z) flank (z, 10000,start=FALSE)); I am writing to find out if someone has a suggestion for a faster way of doing this? With 40000 el ...
bsgenome written 6.2 years ago by Lakshmanan Iyer250 • updated 6.2 years ago by Martin Morgan ♦♦ 20k
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Comment: C: Bioconductor 2.6 is released
... Could any one share instrctions/info on maintaining both the release as well as development version of R/bioconductor on an Ubuntu box? It would certainly help folks like me avoid a lot of experimetation and conflict headache. -Best -Lax Sent from my iPhone On Apr 23, 2010, at 5:41 PM, Thomas Girk ...
written 7.5 years ago by Lakshmanan Iyer250

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