[Bioc-sig-seq] readFastq

[Martin Morgan]

On 08/31/2010 06:18 PM, joseph wrote:
> can you import two lanes with the readFastq function to create a single 
> ShortReadQ object? 

Hi Joseph

after

  example(readFastq)

try

  fl = list.files(analysisPath(sp), "s_1_sequence.txt")
  readFastq(fl)
  readFastq(c(fl, fl))

also, something like

  readFastq(analysisPath(sp), "s_[123]_sequence.txt")

would read all files in the directory analysisPath(sp), matching the
pattern (see, e.g., ?list.files) "s_[123]_sequence.txt" into a single
object. Note that this requires enough memory to store all the data.
Also it might be interesting to compare the input speed of something like

  srapply(c(fl, fl), readFastq,
          reduce=function(lst) Reduce(append, lst))

before and after

  library(multicore)

and with larger data files than those provided as examples in the
ShortRead package.

Martin



> 
> Thanks
> Joseph
> 
> 
> 
>       
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> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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