Moderator: Michael Lawrence

gravatar for Michael Lawrence
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Posts by Michael Lawrence

<prev • 1,188 results • page 2 of 119 • next >
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Answer: A: Combine 5' leaders and 1st exon of cds into GRangesList
... Subscripting into cds should work by name, and you can do that in a vectorized way: cdsForUTRs <- cds[names(fiveUTRs)] You can use the `phead()` function to select the first exons without looping: firstExons <- phead(cdsForUTRs, 1L) Then combine them using the element-wise pc(): fiveUT ...
written 27 days ago by Michael Lawrence9.8k
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Comment: C: Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() f
... Unable to reproduce this. Maybe it was just a transient issue, or something to do with your network. Either way, we no longer support your version of Bioconductor. ...
written 5 weeks ago by Michael Lawrence9.8k
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Answer: A: The track cannot show in UCSC
... At some point UCSC changed, so now we have to update rtracklayer. Please wait for the new version in a couple days. ...
written 5 weeks ago by Michael Lawrence9.8k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... This should probably be posted as a separate question. For #1, you could use vmatchPattern() and remove the reads that match. For #2, just remove those with a value of width() less than 100. For #3, you'll probably need to look into readGAlignments() and read the BAM file directly instead of the fas ...
written 6 weeks ago by Michael Lawrence9.8k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... Maybe you could break that down into separate calls? So we can tell whether it is resize, trim or subset? Also, in the future, please just add comments, don't add a new answer. ...
written 6 weeks ago by Michael Lawrence9.8k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... Interesting. Which part is slow, the last extraction? ...
written 6 weeks ago by Michael Lawrence9.8k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... Because I am not good at the offset math, I would have done something like this: si <- Seqinfo(names(dna), width(dna)) gr <- GRanges(vmatchPattern("C", dna), seqinfo=si) window.size <- 11L windows <- subset(trim(resize(gr, window.size, fix="center")), width == window. ...
written 6 weeks ago by Michael Lawrence9.8k • updated 6 weeks ago by Martin Morgan ♦♦ 20k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... Try: which <- GRanges("HIV", resize(ranges(Cpattern), 5L, fix="center"))   ...
written 6 weeks ago by Michael Lawrence9.8k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... The call to IRanges() should be: IRanges(which(genome == DNAString("C")), width=1L) ...
written 6 weeks ago by Michael Lawrence9.8k
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Answer: A: GenomicAlignments - extracting sequence signatures from bam file
... If you have a FASTA file of your HIV genome, read it with something like: genome <- read.DNAStringSet("hiv.fasta")[[1L]] This assumes the genome is a single sequence. ...
written 6 weeks ago by Michael Lawrence9.8k

Latest awards to Michael Lawrence

Scholar 4 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 7 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 7 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 8 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 8 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 8 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 9 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 19 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 19 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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