Moderator: Michael Lawrence

gravatar for Michael Lawrence
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Posts by Michael Lawrence

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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... The problem is not the UTR ranges (those are just ignored) but rather the absence of "exon" ranges. You'll need those for this to work. The GenomicFeatures maintainers might decide to support the utr + CDS way of specifying exons, but currently explicit "exon" ranges are required. ...
written 19 days ago by Michael Lawrence9.9k
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... The issue with the UTRs seems to be that the GenomicFeatures package ignores the three/five_prime_utr features and instead relies on exon features (and their difference from the CDS features). The GFF3 spec says: UTRs, splice sites and translational start and stop sites. These are implied by the ...
written 19 days ago by Michael Lawrence9.9k
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Answer: A: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... Not sure about the TxDb UTR issue. For mapping into the exons, extract the transcript using exonsBy() instead of transcripts(). Also, you'll want to be careful about assigning the ranges (start/end) back into the reads GRanges, because those coordinates will not be valid on the original seqnames.   ...
written 19 days ago by Michael Lawrence9.9k
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Comment: C: Gviz IdeogramTrack fails with Error: failed to load HTTP resource
... Hopefully just a transient issue. This is a simple download of a web page, via the XML package and its embedded nanohttp library (part of libxml2). ...
written 21 days ago by Michael Lawrence9.9k
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Comment: C: issue retrieving metadata after psetdiff function
... The current behavior is intentional. There is not a 1-1 correspondence between the input and output ranges (which required the use of rep() here). Therefore it does not make sense in general to carry over the metadata. ...
written 28 days ago by Michael Lawrence9.9k
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Comment: C: Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad
... You should wait for the new version to appear. ...
written 29 days ago by Michael Lawrence9.9k
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Answer: A: Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad
... This was recently "fixed" in devel and now I have ported it to release, rtracklayer version 1.38.3. ...
written 4 weeks ago by Michael Lawrence9.9k
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Comment: C: GenomicRanges: identify overlapping regions, get intersection between each overl
... I updated my answer. Hopefully it gets you closer. ...
written 4 weeks ago by Michael Lawrence9.9k
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Comment: C: GenomicRanges: identify overlapping regions, get intersection between each overl
... You'll need to provide a reproducible example. ...
written 4 weeks ago by Michael Lawrence9.9k
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Answer: A: GenomicRanges: identify overlapping regions, get intersection between each overl
... This might get you closer, but it's still not clear what you want exactly: ovlp <- read.table("ovlp.txt", header=TRUE) ## Note: no need for renaming nor reordering of columns gr <- makeGRangesFromDataFrame(ovlp, keep.extra.columns = TRUE) hits <- findOverlaps(gr, ignore.strand=TRUE, ...
written 4 weeks ago by Michael Lawrence9.9k

Latest awards to Michael Lawrence

Scholar 7 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 9 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 10 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 10 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 10 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: filtering VCF files
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 11 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 11 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: setdiff for GenomicRanges
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 12 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Operations across Lists of GenomicRanges?
Scholar 22 months ago, created an answer that has been accepted. For A: setdiff between GenomicRanges objects keeping metadata
Scholar 22 months ago, created an answer that has been accepted. For A: Operations across Lists of GenomicRanges?

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