User: smcnulty

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Posts by smcnulty

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Answer: A: Multithreading CopywriteR on SLURM cluster
... I think this may account for part of the problem. I was processing the samples together in CGHcall, but was missing a few on my laptop. I processed 17 BAMs on the cluster but only a subset of those on the laptop. We also found this in the CGHcall documentation (http://www.rdocumentation.org/package ...
written 3.7 years ago by smcnulty0
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Answer: A: Multithreading CopywriteR on SLURM cluster
... Hi Thomas, So, here's the breakdown of my work so far ... As I said before, I'm trying to process 17 BAM files, either as 1 run on my laptop or as 17 separate runs on our cluster. I'm often getting this error at the end of the run: Total calculation time of CopywriteR was: 31.96694 Warning mes ...
written 3.7 years ago by smcnulty0
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Answer: A: Multithreading CopywriteR on SLURM cluster
... I'm still working with the people who manage our cluster to determine which version of CopywriteR was loaded and to get the multi threading up and running, but I'll let you know what comes of it. In the meantime, I'm able to run CopywriteR and CGHcall on individual BAM files, passing each BAM to a ...
written 3.8 years ago by smcnulty0
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Multithreading CopywriteR on SLURM cluster
... Hello, I'm trying to multi-thread CopywriteR on a slurm cluster using openmpi. My jobs seem to be launching properly and run for about 10m, but then they die prematurely. The final message in my slurm output file looks like this: Error in `[<-.data.frame`(`*tmp*`, , "total.properreads", value ...
slurm copywriter openmpi written 3.8 years ago by smcnulty0 • updated 3.7 years ago by t.kuilman140
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Answer: A: Calling amplifications and deletions from CopywriteR output
... You said that you have experience with CGHcall. Would you mind providing some example code as to how you would use the log2_read_counts.igv file as input with CGHcall? I'm reading the vignette now, but I'm a bit confused as to where the CopywriteR output intersects the CGHcall workflow. I'm sorry to ...
written 3.8 years ago by smcnulty0
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Calling amplifications and deletions from CopywriteR output
... I’m very interested in using CopywriteR to detect copy number variation in target capture sequencing data. I’m looking to select a tool to implement in a high-throughput bioinformatic workflow. Therefore, I won’t be able to manually assess each output plot or IGV file. I was hoping to get some advic ...
copy number copywriter written 3.8 years ago by smcnulty0 • updated 3.7 years ago by t.kuilman140

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For Calling amplifications and deletions from CopywriteR output

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