User: Robert K. Bradley

Reputation:
40
Status:
New User
Location:
United States
Twitter:
@bradleybio
Last seen:
5 months ago
Joined:
6 years, 4 months ago
Email:
r*******@fredhutch.org

Posts by Robert K. Bradley

<prev • 39 results • page 1 of 4 • next >
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... Thank you for the suggestion. I will give it a try. ...
written 5 months ago by Robert K. Bradley40
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... Would it be possible to create versions that are compressed with bgzip instead? ...
written 5 months ago by Robert K. Bradley40
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... That's wonderful to hear. Thank you! I think that a solution will benefit many people (and my own group as well). ...
written 5 months ago by Robert K. Bradley40
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... Thank you for the reference. Is the problem that AH134 and other AnnotationHub objects were compressed with razip instead of bgzip? If so, would it be possible to update those files to be stored with bgzip? Many people use those assemblies--some of which correspond to the latest version of the genom ...
written 5 months ago by Robert K. Bradley40
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... Thank you for the reference. Is the problem that AH134 and other AnnotationHub objects were compressed with razip instead of bgzip? If so, would it be possible to update those files to be stored with bgzip? Many people use those assemblies--some of which correspond to the latest version of the genom ...
written 5 months ago by Robert K. Bradley40
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... Thank you for the reply. Would you mind explaining what changed in Rsamtools to prevent parsing of the FASTA files? I didn't see any changes that I would have expected to cause such a problem from the Rsamtools change log. Thank you also for pointing me to the GTF and 2bit files. The GTF files corr ...
written 5 months ago by Robert K. Bradley40
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Comment: C: AH134 and other AnnotationHub objects unavailable as "defunct"
... Thank you for the reply. Would you mind explaining what changed in Rsamtools to prevent parsing of the FASTA files? I didn't see any changes that I would have expected to cause such a problem from the Rsamtools change log. Thank you also for pointing me to the GTF and 2bit files. The GTF files corr ...
written 5 months ago by Robert K. Bradley40
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AH134 and other AnnotationHub objects unavailable as "defunct"
... Hello, I discovered that several AnnotationHub objects corresponding to genome assemblies are no longer available after updating to R 3.6.0. Specifically: > hub = AnnotationHub() snapshotDate(): 2019-04-29 > hub[["AH134"]] Error: Defunct > hub[["AH188"]] Error: Def ...
annotationhub written 5 months ago by Robert K. Bradley40 • updated 5 months ago by shepherl ♦♦ 1.6k
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Comment: C: possible bug resulting in warnings when reading tags with scanBam and ScanBamPar
... Thank you! It's working without problems for me now. ...
written 15 months ago by Robert K. Bradley40
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Comment: C: possible bug resulting in warnings when reading tags with scanBam and ScanBamPar
... My sessionInfo is below (I couldn't include it in the above response due to the character limit): > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS attached base packages: [1] stats4 parallel grid grDevices utils ...
written 15 months ago by Robert K. Bradley40

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