## User: Sang Chul Choi

Reputation:
230
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Trusted
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Last seen:
7 years, 3 months ago
Joined:
7 years, 8 months ago
Email:
s****@cornell.edu

#### Posts by Sang Chul Choi

<prev • 22 results • page 1 of 3 • next >
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... Hi, Turning off kmer option resolves the issue of variable length reads. Thank you, SangChul ________________________________ From: Vince S. Buffalo [vsbuffalo@gmail.com] Sent: Wednesday, June 06, 2012 2:25 PM To: Sang Chul Choi Cc: bioconductor Subject: Re: [BioC] qrqc with variable length of s ...
written 7.3 years ago by Sang Chul Choi230
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... Thank you for offering help. Appended are the R script and its output mostly from sessionInfo() function. Thank you, SangChul The R script: ====================================================================== ================== library(qrqc) args <- commandArgs(trailingOnly = TRUE) if (lengt ...
written 7.3 years ago by Sang Chul Choi230
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... I have tried to tunn off the option when reading sequences of variable lengths in a gzipped FASTQ file (2GB) using readSeqFile. The computer has 16 GB memory, and it used up all of the memory, leaving R in "Dead" or not running any more. Is there a way of sidestepping this problem? Thank you, San ...
written 7.3 years ago by Sang Chul Choi230
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... Hi, I am using qrqc to plot base quality of a short read fastq file. When the FASTQ file has short reads of the same length, the readSeqFile could read in the FASTQ file (25 millions of 100bp reads) with a couple of GB of memory. I trimmed 3' end of the short reads, which would lead to short reads ...
written 7.3 years ago by Sang Chul Choi230 • updated 7.3 years ago by Thomas Girke1.7k
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... Thank you for the helpful message. I followed it, and it worked. Thank you, SangChul On May 31, 2012, at 10:40 AM, James W. MacDonald wrote: > Hi SangChul, > > On 5/31/2012 9:29 AM, Sang Chul Choi wrote: >> Hi, >> >> Thank you for the helpful replies. >> >> ...
written 7.3 years ago by Sang Chul Choi230
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... Hi, Thank you for the helpful replies. The command line that causes the problem is: makeReport(fq.file, outputDir=bwadir) from qrqc package. I do not know what parts in makeReport of qrqc R package cause the problem. Appended are outputs of capabilities() run at the head and compute nodes. A ses ...
written 7.3 years ago by Sang Chul Choi230
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... Hi, I am trying to use qrqc Bioc package in a linux machine used as a compute node. I have the following error: ==================== Error in X11(paste("png::", filename, sep = ""), g$width, g$height, pointsize, : unable to start device PNG In addition: Warning message: In grDevices::png(..., ...
written 7.3 years ago by Sang Chul Choi230 • updated 7.3 years ago by James W. MacDonald51k
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... Hi, I wish to smooth rugged coverage of short reads by using seqbias R package. I followed the vignette of seqbias R package to see some bias in mapping of short reads from experiment. I computed bias values for each site of a bacterial genome using the package. Because each site is given a bias ...
written 7.4 years ago by Sang Chul Choi230 • updated 7.4 years ago by Martin Morgan ♦♦ 23k
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... Hi, I made a TranscriptDb object, which worked fine when I use it in the same R session. I want to reuse it by saving the object and loading it in another R session. I got an error like following: > txdb <- makeTranscriptDb (transcripts, splicings, chrominfo=chrominfo) > save(txdb, file= ...
written 7.5 years ago by Sang Chul Choi230 • updated 7.5 years ago by Malcolm Cook1.5k
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... I might answer to my question. Maybe I could just set "+" to all of the features not "*". I think strand(GappedAlignments object) <- '+' would set '+' to all of the reads. But, I will appreciate if someone answer whether this approach would do what I want. Thank you, SangChul On Apr 5, 2012, ...
written 7.5 years ago by Sang Chul Choi230

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