ShortRead package

[bioinfosm]

Hi,

Any experiences with the ShortRead R package?

http://bioconductor.org/packages/2.3/bioc/vignettes/ShortRead/inst/doc/Overview.pdf

I can finally make it to run, but people's experience using it, tweaking it, and QC.ing data from the functions will be helpful..

sm

[bioinfosm]

<bump>

Also more stuff coming out in R for NGS data

http://bioconductor.org/workshops/2008/SeattleNov08/

[archi]

I'm getting the following errors in using the readFastq function
readFastq("home/linux/sratoolkit.2.34-2-centos_linux64/bin",pattern="SRR039194_1.fastq")
Error: Input/Output
no input files found
dirPath: home/linux/sratoolkit.2.34-2-centos_linux64/bin
pattern: SRR039194_1.fastq

any suggestions on how to fix this?
please reply asap
thanks!

[GenoMax]

You may be missing a leading "/" in your path home/linux/sratoolkit.2.34-2-centos_linux64/bin. Are the sequence files in this path?

[archi]

I'm able to generate the fastq version of the sra file in the terminal.But how do I save its copy in my computer??

please reply asap

[GenoMax]

Have you looked in the same directory where your SRA file was?

[archi]

okay,got it.
thanks

[archi]

While using ShortRead package to read a fastq file what are the exact arguments to be put in the readFastq function?
and how do we segregate from so many reads only those which have a particular sequence?

[mastal]

If you type '?readFastq' at the R prompt on the commandline, you should get a help page that explains the usage for the function.

Download the manuals for the ShortRead package from:

http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html

I think that readFastq() can only be used to read in complete fastq files, but then you can apply various filters to the data to get only the reads you want. See the documentation.

[archi]

I have around 4 Lac lines in my fastq file.So while using readFastq I'm constantly getting an error message of unexpected number of lines.
Can someone please suggest how do I manipulate my reads now,my final aim is to get a set of reads which have a particular sequence at the end.

please reply asap