Hi All

 

I have recently started to acquaint my self with new R packages for NGS
data processing/analysis.  I think the community has done a great work
in developing these packages. I must say I am amazingly surprised to see
some of the capabilities. 

 

I have a quick comment.  While playing  with ShortRead package I am not
able to successfully load the export file even one for that matter. I am
using a single PC to do this .  I belv it has It has sufficient memory
(4 GB) to handle one lane of data.  I waited for 15-18 minutes before my
pc started to show sign of sickness. I eventually had to kill the
process.

 

Here is wat I did.

 

Library(ShortRead)

sp=SolexaPath("/local/seq_archive/solexa/090309_HWI-EAS397_0006")

path=analysisPath(sp)[4]  ### I just wanted to look at one GERALD
folder.

aln=readAligned(path,type="SolexaExport","s_6_export.txt")

GOT STUCK HERE

 

Is there anything I am doing the wrong way. Please let me know.  

 

Cheers,

-Abhi

----------------------------- 
Abhishek Pratap 
Bioinformatics Software Engineer 
Institute for Genome Sciences <http://www.igs.umaryland.edu/>  
School of Medicine, Univ of Maryland 
801, W. Baltimore Street, Baltimore, MD 21209 
Ph: (+1)-410-706-2296 







 

 


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