how to read .bam file

[孟欣]

Hi all:
I've got a data of ".bam" which is created from my partner under linux sysyem.
My system is window xp, and I wanna know how to read the .bam file.
 
 
Many thanks!
 
 
My best
        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Peter Dalgaard-2]

On Aug 10, 2012, at 08:24 , mengxin wrote:

> Hi all:
> I've got a data of ".bam" which is created from my partner under linux sysyem.
> My system is window xp, and I wanna know how to read the .bam file.
>

An what is the .bam file supposed to contain? You are really not giving us much of a clue, are you?

I'd venture a guess that it is something with genomic alignment files, in which case you need to see the Bioconductor folks over on their mailing lists. However, it could be a multitude of other things, like "Bob's Adlib Music" of "Bravo Archived Media"...

--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: [phone]
Email: [hidden email]  Priv: [hidden email]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[孟欣]

Yes,it's genomic alignment files.
 
Thanks for your help.


 



At 2012-08-10 18:10:02,"peter dalgaard" <[hidden email]> wrote:

>
>On Aug 10, 2012, at 08:24 , mengxin wrote:
>
>> Hi all:
>> I've got a data of ".bam" which is created from my partner under linux sysyem.
>> My system is window xp, and I wanna know how to read the .bam file.
>>
>
>An what is the .bam file supposed to contain? You are really not giving us much of a clue, are you?
>
>I'd venture a guess that it is something with genomic alignment files, in which case you need to see the Bioconductor folks over on their mailing lists. However, it could be a multitude of other things, like "Bob's Adlib Music" of "Bravo Archived Media"...
>
>--
>Peter Dalgaard, Professor
>Center for Statistics, Copenhagen Business School
>Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>Phone: [phone]
>Email: [hidden email]  Priv: [hidden email]
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Rui Barradas]

Hello,

#install.packages('sos')  # do this,
library(sos)   # it would have saved you hours.

r1 <- findFn('sam')
r2 <- findFn('bam')

r1 & r2

Number one. Genomic alignment file formats.

Hope this helps,

Rui Barradas

Em 10-08-2012 11:10, peter dalgaard escreveu:

> On Aug 10, 2012, at 08:24 , mengxin wrote:
>
>> Hi all:
>> I've got a data of ".bam" which is created from my partner under linux sysyem.
>> My system is window xp, and I wanna know how to read the .bam file.
>>
> An what is the .bam file supposed to contain? You are really not giving us much of a clue, are you?
>
> I'd venture a guess that it is something with genomic alignment files, in which case you need to see the Bioconductor folks over on their mailing lists. However, it could be a multitude of other things, like "Bob's Adlib Music" of "Bravo Archived Media"...
>

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Martin Morgan]

On 08/09/2012 11:24 PM, mengxin wrote:
> Hi all:
> I've got a data of ".bam" which is created from my partner under linux sysyem.
> My system is window xp, and I wanna know how to read the .bam file.

See Bioconductor Rsamtools

   http://bioconductor.org/packages/release/bioc/html/Rsamtools.html

Martin

>
>
> Many thanks!
>
>
> My best
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: [phone]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.