search for: shortread

Dear folks, Please welcome a newbie both to R and the mailing list :). I am currently working on a sequencing project, and heard about R as well as some of its packages for next gen sequencing, and decided to give it a try. Starting with ShortRead, I found a document (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention that readAligned was extended to support SAM format (for example, BWA output). So I tried readAligned with BWAAln <- readAligned(BWAFile, type = &...

Hi, I understand ShortRead::FastqStreamer will read chunks in parallel depending on the value of ShortRead:::.set_omp_threads I see this discussed here: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004355.html and nowhere else. It probably should be documented in ShortRead. Possibly this has already changed for I a...

Dear R-Help, I would be most grateful if you could inspect the attached install file. I would like to be able to use ShortRead to generate QA reports for Genome Analyzer output data. OS: Linux CentOS 5.3 on HP Proliant server . In process of installing "R" package after configuration flagging some missing modules-libraries the install process will not perform 'make' function. Also there is a problem with...

Hi, I want to group a large list (20 million) of strings into categories based on string similarity? The specific problem is: given a list of DNA sequence as below ACTCCCGCCGTTCGCGCGCAGCATGATCCTG ACTCCCGCCGTTCGCGCGCNNNNNNNNNNNN CAGGATCATGCTGCGCGCGAACGGCGGGAGT CAGGATCATGCTGCGCGCGAANNNNNNNNNN CAGGATCATGCTGCGCGCGNNNNNNNNNNNN ...... ..... NNNNNNNCCGTTCGCGCGCAGCATGATCCTG

...wt7k7g9zsjr4dha6f1c > > > > >>>> On Tue, Oct 23, 2012 at 12:13 PM, Steve Lianoglou < >>>> mailinglist.honeypot at gmail.com**> wrote: >>>> >>>> In response to a question from yesterday, I pointed someone to the >>>>> ShortRead `srapply` function and I wondered to myself why it had to >>>>> necessarily by "burried" in the ShortRead package (aside from it >>>>> having a `sr` prefix). >>>>> >>>> >>> I don't know that srapply necessarily 'got...

Hello everyone. There is a new competition, outlined on the blog dataists<http://www.dataists.com/2010/10/using-data-tools-to-find-data-tools-the-yo-dawg-of-data-hacking/>, inviting us to analyse statistics of the use of R packages (collected from 52 R users), to create a R-package suggestion engine for ourselves. Since I noticed several bloggers already wrote about it (as I have detailed

Hello all, I upgraded my R workstation, and to my dismay, only one core appears to be used during intensive computation of a bioconductor function. What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When I fully load it, top reports about 25% user, 75% idle and 0.98 short-term load. The archives gave nothing helpful besides mention of snow. I thought of posting to HPC, but this system

I have a two part question Part 1) I am trying to remove characters in a string based on the position of a key character in another string.? I have a solution that works but it requires a for-loop.? A vectorized way of doing this has alluded me.? CleanRead<-function(x,y) { ? if (!is.character(x)) ??? x <- as.character(x) ? if (!is.character(y)) ??? y <- as.character(y) ?

...ge passes R CMD check! Presumably because R CMD check installs the package first. This took me a long time to track down (inspired by a recent addition of dataset to the Bioconductor package Genominator and a subsequent failed build - specifically the dataset yeastAnno.sources and the vignette withShortRead.Rnw). I am using lazy loading (in case it matters, which I don't think it does). It seems like the relevant fix is to include pdf versions of the vignette(s) in inst/doc. On one hand I can see why the build fails. And the fix is easy. But just thought I would mention it. Kasper