[R] ShortRead with BWA

Duke duke.lists at gmx.com
Wed Apr 28 00:07:43 CEST 2010

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 
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?



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