User: Robert K. Bradley

Reputation:
40
Status:
New User
Location:
United States
Twitter:
@bradleybio
Last seen:
4 days, 20 hours ago
Joined:
5 years, 11 months ago
Email:
r*******@fredhutch.org

Posts by Robert K. Bradley

<prev • 38 results • page 1 of 4 • next >
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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 4 days 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 16 days 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 17 days 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 17 days 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 17 days 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 17 days 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 18 days ago by Robert K. Bradley40 • updated 18 days ago by shepherl ♦♦ 1.4k
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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 10 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 10 months ago by Robert K. Bradley40
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Comment: C: possible bug resulting in warnings when reading tags with scanBam and ScanBamPar
... Martin, thank you for the quick response and fix. I updated Rsamtools per your instructions. I no longer gett the above warning message. However, I think that a new bug may have been introduced. I can read in the BAM version of the following SAM file without problems if I don't specify parameters: ...
written 10 months ago by Robert K. Bradley40

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