User: Chao-Jen Wong
Chao-Jen Wong • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- USA/Seattle/Fred Hutchinson Cancer Research Center
- Last seen:
- 4 months, 3 weeks ago
- Joined:
- 4 years, 4 months ago
- Email:
- c****@fredhutch.org
Posts by Chao-Jen Wong
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... Thank Matin. That straighten out my confusion!!!
(Hi Martin!)
...
written 4 months ago by
Chao-Jen Wong • 30
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... Thank you, Mike. But registryargs only takes arguments ‘file.dir’, ‘work.dir’, ‘packages’, ‘namespaces’, ‘source’, ‘load’, and ‘make.default’. It is not for resrouces vaiables. When I set cluster="slurm", BatchtoolsParam uses batchtool's default template(batchtoolsTemplate("slurm")). So here is my c ...
written 4 months ago by
Chao-Jen Wong • 30
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... Mike, thanks for your prompt help. I still run into the problems. It seems like resources is not a valid argument for BatchtoolsParam. Here is my code to include resource as an input argument for the BatchtoolsParam constructor:
param <- BatchtoolsParam(worker=4, cluster="slurm",
...
written 5 months ago by
Chao-Jen Wong • 30
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... I want to use "BatchtoolsParam" to parametrize schedule options on slurm backend. When using slurm backend, the template slurm-simpl.tmpl provided by batchtools is used to parametrize sbatch variables. My problem is that I cannot find a way to pass the resources variable to the template;
Here is my ...
written 5 months ago by
Chao-Jen Wong • 30
• updated
5 months ago by
Mike Smith • 3.3k
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... Thanks a lot. I did not know that. ha......
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written 2.0 years ago by
Chao-Jen Wong • 30
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... FYI, I use makeTxDbFromBiomart() instead and get the right gene IDs and transcripts. However, the metadata was wrong due to error detected by .Ensembl_getMySQLCoreDir(), which is not a big deal. sessionInfo() is the same as above. Thanks.
> txdb <- makeTxDbFromBiomart(biomart="ENSEMBL_MAR ...
written 2.0 years ago by
Chao-Jen Wong • 30
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... As I was using the TxDb.Mmusculus.UCSC.mm10.ensGene package installed using biocLite(), the ID appears to be neither Eensembl ID nor EntrezID. I believe those gene IDs are wrong. (I am using Bioconductor 3.5 on R/3.4, and all the packages are just updated. see sessionInfo() below.)
> library(Tx ...
written 2.0 years ago by
Chao-Jen Wong • 30
• updated
2.0 years ago by
James W. MacDonald ♦ 49k
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... Hi, Michael,
I just pileup() and it seems to work for my purpose. I parse the return the data.frame of pileup() and compare with the reference genome to define the type of mismatch. I have not tried tallyVariants(), but it sounds even better. I will definitely try it tomorrow. Thanks for the help ...
written 2.2 years ago by
Chao-Jen Wong • 30
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... Hi, bioconductor members,
I have two questions here. The first one is basically about how to use narrow() to keep the wanted sequence in an efficient way. I have a read and corresponding cigar, a subset from my GAlignments instance. I want to clip the insertion and soft-clip from the read so that ...
written 2.2 years ago by
Chao-Jen Wong • 30
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... Thank you, Michael, for the helpful details. Converting with grglist() using drop.D.ranges=TRUE before calling findoverlaps() would definitely work for my case. Wouldn't have known this before.
Thanks,
CJ
...
written 2.2 years ago by
Chao-Jen Wong • 30
Latest awards to Chao-Jen Wong
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: Combining .idat and GEO data sets in minfi
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