Admin: Valerie Obenchain
Valerie Obenchain ♦♦ 6.4k
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Posts by Valerie Obenchain
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... Hi,
I think your question is why is there a count for Union when a read overlaps with multiple ranges in a single element of a GRangesList. That's the question I'll answer - if that's wrong, please clarify.
An element of a GRangesList is considered a single feature. If a read overlaps with any of ...
written 9 days ago by
Valerie Obenchain ♦♦ 6.4k
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... If you're calling summarizedOverlaps with the reads in a GAlignmentsPairs then yes, this would be the way to go. If instead the reads are in a BAM file they will be read into different classes depending on the value of the fragments argument.
When you provide a BAM file of paired-end reads with fra ...
written 11 days ago by
Valerie Obenchain ♦♦ 6.4k
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... Hi Shraddha,
It's best to use the most current package versions as they will contain bug fixes. A bug was identified in distanceToNearest() a few months ago and has been fixed in the release and devel branches. To see what version a package is at in release and devel check the build report:
https: ...
written 11 days ago by
Valerie Obenchain ♦♦ 6.4k
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... Developers and Community Members,
The release of Bioconductor 3.7 will be on Tuesday, May 1, 2018. Please see the schedule for details:
https://www.bioconductor.org/developers/release-schedule/
Over the next month key deadlines will be announced on the bioc-devel mailing list:
https://stat.ethz. ...
written 29 days ago by
Valerie Obenchain ♦♦ 6.4k
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... Sounds like you may have out of date packages. Please run BiocInstaller::biocValid(), update old packages and let us know if the error persists.
Valerie
...
written 4 weeks ago by
Valerie Obenchain ♦♦ 6.4k
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... Are you still having this problem? After you
source("https://bioconductor.org/biocLite.R")
what happens when you call
library(BiocInstaller)
Valerie
...
written 8 weeks ago by
Valerie Obenchain ♦♦ 6.4k
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... Hi,
The ?GNCList man page in GenomicRanges has examples of overlaps with circular sequences. See the "With Circular Sequences" section at the bottom.
The range to overlap should extend past the end of the circular sequence, not start again at '1'. In your example above the range would start at 165 ...
written 8 weeks ago by
Valerie Obenchain ♦♦ 6.4k
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... That's a pretty thorough discussion on the page you reference. In one of the responses I specify that overlap only requires one base.
Are you also using bedtools? Are you seeing some kind of inconsistency? It would be good to see a code example if you have a specific question.
Valerie
Edit: Spe ...
written 9 weeks ago by
Valerie Obenchain ♦♦ 6.4k
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... Hi,
Thanks for your patience. This is now fixed in GenomicRanges 1.31.3 in devel and 1.30.1 in release. Both should be available via biocLite() tomorrow around 3pm EST.
The bug was hitting the case where a '*' query followed both a '+' and '-' range in subject. Instead of choosing the closest rang ...
written 4 months ago by
Valerie Obenchain ♦♦ 6.4k
0
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135
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... Hi,
The result of locateVariants() is a "reped out" GRanges; one row for each variant-transcript match. To add the query metadata to the result you could rep out the metadata in the query using the 'QUERYID' column from the result. From the man page,
‘QUERYID’ The ‘QUERYID’ column provides a ...
written 4 months ago by
Valerie Obenchain ♦♦ 6.4k
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For A: about collapsed and expanded vcf file
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For A: about collapsed and expanded vcf file
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For A: about collapsed and expanded vcf file
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For merging VCF files
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15 months ago,
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For A: about collapsed and expanded vcf file
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15 months ago,
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For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
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For A: BiocParallel example does not work any more (sbatch produced exit code 1)
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For A: Genomic features for genomic positions
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For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
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For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
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For A: AnnotationHub: two broad peaks from same url are not the same
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For A: inconsistent default of file suffix
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For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
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For A: Genomic features for genomic positions
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For A: readGAlignmentPairs slow in problematic region
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For A: AnnotationHub: two broad peaks from same url are not the same
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For A: Intersecting a Granges and a GRangesList using within
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For A: inconsistent default of file suffix
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