User: Jonathan Griffiths

Reputation:
30
Status:
New User
Location:
Cambridge UK
Twitter:
omnislip
Scholar ID:
Google Scholar Page
Last seen:
2 months ago
Joined:
6 months ago
Email:
j********************@gmail.com

Posts by Jonathan Griffiths

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Recommendations for running DropletUtils::swappedDrops() on multiplexed samples
... Are the UMI and cell barcodes are the same between the 5' library and 3' library, and they are stored in the same way in the molecule_info file? Or did you institute some sort of 10X version check? This will have obvious implications for whether `swappedDrops` is easily able to detect that you are t ...
written 5 months ago by Jonathan Griffiths30
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Comment: C: Is there a limitation to the number of cells swappedDrops can handle?
... Hi Joon, Can you provide some more information about how you ran swappedDrops (e.g., locally or on a compute cluster), and whether there was an error message that was reported? Loading in very many unfiltered matrices from CellRanger should be quite tough on your RAM. Are you running in an environ ...
written 5 months ago by Jonathan Griffiths30
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Comment: C: subread gives segfaults when supplied with falsely-identified paired end reads
... Indeed, regenerating my index fixed this (though there was no apparent error while it was being made). Thanks for the clarity here! ...
written 6 months ago by Jonathan Griffiths30
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subread gives segfaults when supplied with falsely-identified paired end reads
... Hello, I was mapping some poorly annotated RNA-seq data using subread and incorrectly understood it to be paired end data. Supplying the fastq files as PE reads to `subread-align` caused a near-instant segfault. Should it provide a clearer error message? I can supply some offending files if you l ...
rsubread subread written 6 months ago by Jonathan Griffiths30 • updated 6 months ago by Gordon Smyth38k
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Comment: C: Usage of doubletCells() function before or after the batch correction?
... double post, oops... ...
written 6 months ago by Jonathan Griffiths30
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Comment: C: Usage of doubletCells() function before or after the batch correction?
... I have recently been through this for a set of many 10X samples (what I ended up doing is [shown here][1]) In essence, I first calculated the scores and called doublets within samples, then performed another round of calling across all samples to identify where I had missed calls in individual samp ...
written 6 months ago by Jonathan Griffiths30

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