[Bioc-sig-seq] using shortRead for Bowtie alignments

[James Bullard]

You can just specify the filename directly as the first argument, so  
something like:

readAligned("reads/mut_1_f.fastq.bowtie", type = "Bowtie")

works on the following setup.

 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-08-11 r49153)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ShortRead_1.3.25   lattice_0.17-25    BSgenome_1.13.10    
Biostrings_2.13.32
[5] IRanges_1.3.53

loaded via a namespace (and not attached):
[1] Biobase_2.5.5 grid_2.10.0   hwriter_1.1   tools_2.10.0

On Aug 20, 2009, at 4:45 PM, burak kutlu wrote:

> Hi Is there a way to specify the actual file name when calling  
> readAligned for bowtie alignments? Instead of the dirPath?
> Thanks
> -burak
>
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