[BioC] a question about girafe

[Sean Davis]

On Fri, Jul 1, 2011 at 10:55 PM, chun-jiang he <camelbbs at gmail.com> wrote:
> Thanks Sean. But I dont know where I can input my .sam file.

Well, you'll want to convert your .sam file to a sorted .bam file and
then index the .bam file (use samtools to do that, for instance).
Then, you can use the readAligned() function from the ShortRead
package.  In the girafe vignette, you can see section 2.2 for an
example.

Sean


> On Fri, Jul 1, 2011 at 9:48 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he <camelbbs at gmail.com> wrote:
>> > Hi,
>> >
>> > Does anybody use girafe to analyze .sam file extracting from bowtie.
>> >
>> > Some example is better.
>>
>> Hi, Jiang.  Have you looked at the vignette for the girafe package?
>>
>>
>> http://www.bioconductor.org/packages/release/bioc/vignettes/girafe/inst/doc/girafe.pdf
>>
>> It does include examples.  If you have problems, send the code that
>> you have tried, the error messages, and the output of sessionInfo().
>>
>> Sean
>>
>>
>> > thanks so much,
>> >
>> > Jiang
>> >
>> >        [[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
>> >
>>
>
>        [[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
>