convertion from SAM to BAM

0

Entering edit mode

João Moura ▴ 160

@joao-moura-4505

Last seen 10.3 years ago

Hello, Do you know any way of convertin SAM to BAM using bioconductor? Thanks in advance, -- João Moura [[alternative HTML version deleted]]

• 4.5k views

ADD COMMENT • link updated 13.7 years ago by Sean Davis 21k • written 13.7 years ago by João Moura ▴ 160

0

Entering edit mode

Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

On Tue, Apr 26, 2011 at 8:52 AM, Jo?o Moura <palerma at="" gmail.com=""> wrote: > Hello, > > Do you know any way of convertin SAM to BAM using bioconductor? Hi, Joao. Untested: system(sprintf("samtools view -bS %s > %s",samfilename,bamfilename)) Sean

ADD COMMENT • link 13.7 years ago Sean Davis 21k

0

Entering edit mode

Thank you Sean and Paul, Actually I was looking for something to using in R without calling samtools. Thanks, On Tue, Apr 26, 2011 at 3:13 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Tue, Apr 26, 2011 at 8:52 AM, João Moura <palerma@gmail.com> wrote: > > Hello, > > > > Do you know any way of convertin SAM to BAM using bioconductor? > > Hi, Joao. > > Untested: > > system(sprintf("samtools view -bS %s > %s",samfilename,bamfilename)) > > Sean > -- João Moura [[alternative HTML version deleted]]

ADD REPLY • link 13.7 years ago João Moura ▴ 160

0

Entering edit mode

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 -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

ADD REPLY • link 13.7 years ago Steve Lianoglou ★ 13k

0

Entering edit mode

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

ADD REPLY • link 13.7 years ago Martin Morgan 25k

0

Entering edit mode

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]]

ADD REPLY • link 13.7 years ago João Moura ▴ 160

0

Entering edit mode

Paul Geeleher ★ 1.3k

@paul-geeleher-2679

Last seen 10.3 years ago

Not sure if you can do it from within Bioconductor, but the command line tool samtools will let you do it. If you really need to do it from within R I suppose you could call samtools from R. Paul. On Tue, Apr 26, 2011 at 1:52 PM, Jo?o Moura <palerma at="" gmail.com=""> wrote: > Hello, > > Do you know any way of convertin SAM to BAM using bioconductor? > > Thanks in advance, > > -- > Jo?o Moura > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com

ADD COMMENT • link 13.7 years ago Paul Geeleher ★ 1.3k

Login before adding your answer.