User: alexgraehl

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alexgraehl10
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United States
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1 year, 9 months ago
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Posts by alexgraehl

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CRISPRseek R package: description of output fields that are unclear
... Hi,  CRISPRSeek, an R package for finding suitable guide RNAs (sgRNAs) for CRISPR targeting, has a lot of output files with partially-undocumented column names. These things may be obvious to a CRISPR expert, but for me, some of the columns are still a mystery.  If anyone else has observations abo ...
crisprseek R sgrna crispr written 22 months ago by alexgraehl10 • updated 21 months ago by Julie Zhu3.8k
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Q: I notice that there are two terms used: gRNAefficacy calculategRNAEfficacy calculategRNAEfficiency These both appear in the documentation, and are of course both possible valid words! I am assuming that one of these is a typo, and that "efficiency" is the preferred terminology? ...
written 2.0 years ago by alexgraehl10
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... I end up with this error result (see bold part below). I assume this has something to do with filenames / connections, but I'm not sure what exactly causes this error. Possibly next time I will run the script with "options(error=recover)" to try to diagnose it. This is a very long-running job, thoug ...
written 2.0 years ago by alexgraehl10
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Comment: C: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Thanks for the comment! I totally agree that it is worth being not overly-optimistic about the chances of successfully running not-updated packages. In this particular case, I was also wary of this old package, but manual installation of Vienna + GeneRfold + data.table + GeneR actually did seem (at ...
written 2.0 years ago by alexgraehl10
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Current status: even with 4 2 GHz Xeon cores running over the weekend, but after 3 days, not much headway has been made on my 2 megabase region of interest. Maybe this region is just way too big to be even remotely reasonable? I ran CRISPRSeek with multicore enabled, and each of the four multi-core ...
written 2.0 years ago by alexgraehl10
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Current status: even with 4 2 GHz Xeon cores running over the weekend, but after 3 days, not much headway has been made on my 2 megabase region of interest. Maybe this region is just way too big to be even remotely reasonable? I ran CRISPRSeek with multicore enabled, and each of the four multi-core ...
written 2.0 years ago by alexgraehl10
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Comment: C: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... I will do that, thanks! It appears that GeneRFold also has a dependency on Vienna: configure: error: viennaRNA library >= 1.5 requiered http://www.tbi.univie.ac.at/~ivo/RNA/ ERROR: configuration failed for package 'GeneRfold' * removing '/usr/lib64/R/library/GeneRfold' ...
written 2.1 years ago by alexgraehl10
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Bug report and proposed solution: multicore=TRUE will *ALWAYS* fail on a server with a very large number of cores. (Specifically, I am running this on a machine with 160 cores, which is greater than the maximum allowed number of file connections (128).) Here is the issue: A maximum of 128 connecti ...
written 2.1 years ago by alexgraehl10
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... It appears that I have 128 sockets on this machine. I was trying to run a 2 megabase region, so perhaps the region is too large or it gets split too many ways? Possibly the "multicore" could pick a lower and/or user-defined limit? > showConnections(all=T) 125 "<-localhost:11096" "sockconn" " ...
written 2.1 years ago by alexgraehl10
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Also, I have always had to set "multicore = FALSE," or I always get this error: Error in do.call(rbind, lapply(1:length(subjects), function(p) { :    error in evaluating the argument 'args' in selecting a method for function 'do.call': Error in socketConnection("localhost", port = port, server = T ...
written 2.1 years ago by alexgraehl10

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