User: Chao-Jen Wong

gravatar for Chao-Jen Wong
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

<prev • 34 results • page 1 of 4 • next >
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Comment: C: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
... Thank Matin. That straighten out my confusion!!! (Hi Martin!) ...
written 4 months ago by Chao-Jen Wong30
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Comment: C: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
... 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 Wong30
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Comment: C: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
... 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 Wong30
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BioParallel::BatchtoolsParam() - how to pass customized resource variables to batchtool's "slurm-simple" template using BatchtoolsParam()?
... 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 ...
biocparallel batchtoolsparam written 5 months ago by Chao-Jen Wong30 • updated 5 months ago by Mike Smith3.3k
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Comment: C: Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... Thanks a lot. I did not know that. ha...... ...
written 2.0 years ago by Chao-Jen Wong30
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Comment: C: Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... 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 Wong30
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Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... 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 ...
genomicfeatures txdb written 2.0 years ago by Chao-Jen Wong30 • updated 2.0 years ago by James W. MacDonald49k
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Comment: C: How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequenc
... 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 Wong30
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How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequence?
... 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 ...
genomicalignments narrow mismatch written 2.2 years ago by Chao-Jen Wong30
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Comment: C: GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after
... 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 Wong30

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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