User: Sang Chul Choi

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Posts by Sang Chul Choi

<prev • 22 results • page 1 of 3 • next >
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Comment: C: qrqc with variable length of short reads? - readSeqFile could not handle a 2GB z
... 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 5.5 years ago by Sang Chul Choi230
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Comment: C: qrqc with variable length of short reads? - readSeqFile could not handle a 2GB z
... 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 5.5 years ago by Sang Chul Choi230
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Comment: C: qrqc with variable length of short reads? - readSeqFile could not handle a 2GB z
... 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 5.5 years ago by Sang Chul Choi230
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qrqc with variable length of short reads? - readSeqFile could not handle a 2GB zipped file.
... 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 ...
qrqc written 5.5 years ago by Sang Chul Choi230 • updated 5.5 years ago by Thomas Girke1.6k
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qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?
... 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. >> >> ...
go qrqc assign written 5.5 years ago by Sang Chul Choi230
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Comment: C: qrqc with error message of "unable to start device PNG" and "unable to open conn
... 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 5.5 years ago by Sang Chul Choi230
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qrqc with error message of "unable to start device PNG" and "unable to open connection to X11 display"?
... 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(..., ...
qrqc written 5.5 years ago by Sang Chul Choi230 • updated 5.5 years ago by James W. MacDonald45k
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seqbias : how to correct weight of mapped short reads?
... 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 ...
coverage iranges seqbias written 5.6 years ago by Sang Chul Choi230 • updated 5.6 years ago by Martin Morgan ♦♦ 21k
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load a TranscriptDb object in another R session?
... 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= ...
transcriptdb written 5.7 years ago by Sang Chul Choi230 • updated 5.7 years ago by Malcolm Cook1.4k
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Answer: A: GenomicRanges::summarizeOverlaps without strands?
... 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 5.7 years ago by Sang Chul Choi230

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