On 04/26/2011 06:26 AM, Steve Lianoglou wrote: > Hi, > > On Tue, Apr 26, 2011 at 9:17 AM, Jo?o Moura<palerma at="" gmail.com=""> wrote: >> Thank you Sean and Paul, >> >> Actually I was looking for something to using in R without calling samtools. > > To convert sam -> bam without leaving the comfort of your aRm chair, try: > > R> library(Rsamtools) > R> ?asBam > > Scan the docs to see how asBam works. > > I'm not sure when that was added. If you don't see it in your install, > maybe you need to be running R-2.13 and bioc 2.8 Rsamtools tries to keep it's NEWS file up-to-date, so > news(package="Rsamtoools") Changes in version 1.4.0: NEW FEATURES ... o asBam converts SAM files to (indexed) BAM files Martin > > -steve > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Hi, That's great, thank you! On Tue, Apr 26, 2011 at 3:26 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Tue, Apr 26, 2011 at 9:17 AM, João Moura <palerma@gmail.com> wrote: > > Thank you Sean and Paul, > > > > Actually I was looking for something to using in R without calling > samtools. > > To convert sam -> bam without leaving the comfort of your aRm chair, try: > > R> library(Rsamtools) > R> ?asBam > > Scan the docs to see how asBam works. > > I'm not sure when that was added. If you don't see it in your install, > maybe you need to be running R-2.13 and bioc 2.8 > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- João Moura [[alternative HTML version deleted]]