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

[burak kutlu]

Hi Morgan
It actually works. I should have tried it first.
On the other, it's a good thing that you updated the documentation to indicate that this is possible.
Many thanks
-burak


----- Original Message ----
From: Martin Morgan <mtmorgan at fhcrc.org>
To: burak kutlu <burak_kutlu at yahoo.com>
Cc: bioc-sig-sequencing at r-project.org
Sent: Thursday, August 20, 2009 5:24:04 PM
Subject: Re: [Bioc-sig-seq] using shortRead for Bowtie alignments

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

Hi Burak --

  readAligned("path/to/file", type="Bowtie")

but if that is not working for you then perhaps you can provide more
information, especially the output of sessionInfo(). As a repeatable
example,

  fl = system.file("extdata", "bowtie", "s_1_aligned_bowtie.txt",
package="ShortRead")
  readAligned(fl, type="Bowtie")

I have updated readAligned documentation in the development version.
Here's my sessionInfo

> sessionInfo()
R version 2.9.1 Patched (2009-07-31 r49053)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] ShortRead_1.2.1   lattice_0.17-25   BSgenome_1.12.3   Biostrings_2.12.8
[5] IRanges_1.2.3

loaded via a namespace (and not attached):
[1] Biobase_2.4.1 grid_2.9.1    hwriter_1.1


Martin

> -burak
> 
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