User: Isaac Virshup

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University of Melbourne
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Posts by Isaac Virshup

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Comment: C: Variance between runs of Rsubread
... That's great! Thanks for looking into this. Will the new version be available with the next release of bioconductor or will it be out separately? ...
written 10 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... Wei, On the recommendation of a co-worker I tried running subread using a single thread to see if that produced deterministic output. I've run it a few times now and have been getting the same output – while multi-threaded output still varies by run. I ran this using conda installed R and Rsubread ...
written 10 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... Wei, have you had a chance to retrieve those files? I'd like to take those files down from my cloudstor drive. Best, –Isaac ...
written 12 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... Not sure if there's quite enough space in my dropbox at the moment... I've uploaded them to CloudStor (should be similar) here: https://cloudstor.aarnet.edu.au/plus/index.php/s/gh2AdmTmhr6Vdox ...
written 13 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... The alignment was against GRCh37.69. How should I send you a link to the files? ...
written 13 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... Session info associated with the linked gist above: R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_M ...
written 13 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... Sorry, but I think there has a been a misunderstanding about my question. I'm seeing differences between alignments generated from a single install of RSubread. I'll add an update to my question to clarify this. ...
written 13 months ago by Isaac Virshup0
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Comment: C: Variance between runs of Rsubread
... I've updated the question to include commands and versions used. I'm not sure what you mean by counting summaries, would you mind clarifying? ...
written 13 months ago by Isaac Virshup0
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Variance between runs of Rsubread
... Hello, I've noticed some differences between the count tables generated by repeated runs of RSubread. Most of the differences are a read or two, but for a few particular genes (so far, only ones in repetitive areas) the discrepancies can be hundreds of counts. Is this expected behavior? If so, has ...
alignment rsubread reproducibility written 13 months ago by Isaac Virshup0

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