Hi Duke --
Quoting Duke <duke.li...@gmx.com>:
Dear folks,
Please welcome a newbie both to R and the mailing list :). I am
currently working on a sequencing project, and heard about R as well as
some of its packages for next gen sequencing, and decided to give it a
try. Starting with ShortRead, I found a document
(http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention that readAligned was extended to support SAM format (for example,
BWA
output).
So I tried readAligned with
BWAAln <- readAligned(BWAFile, type = "BWA")
but then I got error:
BWAAln <- readAligned(BWAFile, type = "BWA")
Error: UserArgumentMismatch
arugment 'type' had value 'BWA' allowable values: 'SolexaExport'
'SolexaAlign' 'SolexaPrealign' 'SolexaRealign' 'SolexaResult'
'MAQMap' 'MAQMapShort' 'MAQMapview' 'Bowtie' 'SOAP'
It looks like ShortRead does not support BWA. Am I right, or what am I
doing wrong? Anybody has any idea?
Welcome to R!
But actually, I should be saying 'welcome to Bioconductor!' and you
should be on the Bioconductor (or Bioc-sig-seq) mailing list
http://bioconductor.org/docs/mailList.html
because ShortRead is a Bioconductor package.
BWA produces SAM files, and SAM files can be processed, using
samtools, to (sorted, indexed) BAM files. And BAM files can be read in
using readAligned in the just released Bioconductor 2.6 packages. It's
worth getting your data into BAM files anyway, e.g., for viewing with
the IGV.
I mentioned 'just released', and although you didn't provide the output of
sessionInfo()
(basically essential for any post) I can see that, although you're a
new-comer, it's time to update your R to version 2.11, and update
Bioconductor to the corresponding version 2.6. You might look at
http://bioconductor.org/docs/install/
While google and trial and error are one way of getting help, you
might as well get the vignettes from the package you have installed
browseVignettes("ShortRead")
and discover the R help system
help.start()
library(ShortRead)
help(package="ShortRead")
?readAligned
It'll be more effective in the long run.
Martin
Thanks,
D.
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