Hello all. I am a long-term R user who has recently switched platforms from Windows to Linux and I am having a hard time with the syntax difference.  I am stuck on something that is likely simple, but I am stuck all the same.  I have aligned short reads using Maq 0.7.1 in RedHat and I have the ‘map’ output files as well as the ‘map.txt’ files obtained by mapview.  I am trying to input the files into Bioconductor using ShortReads, but I can’t seem to read the files in.  I can get ‘readAligned’ to work on Windows, but I need the memory from my Linux computer.   

 

I start by creating the dirPath:

dir <- “~/Desktop/Maq50bp/Map_files”

aln <- readAligned(dir,”s_1_sequence.map”,”MAQMap”)

 

Using this, I get an error that ‘pattern’ must be ‘character(1)’.  Alternately, I define pattern by:

 

pattern <- “s_1_sequence.map”

aln <- readAligned(dir,pattern,”MAQMap”)

 

And I get the error that my directory is not a readable directory.  Though I have the right permissions for this directory.

 

Any insight would be greatly appreciated.

 

Jessica

 

Jessica Ezzell Hunter, MS PhD

Postdoctoral Fellow
Department of Behavioral Neuroscience

Oregon Health & Science University
3181 SW Sam Jackson Park Road

L470
Portland, OR 97239

(503) 220-8262 x51988

 


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