[BioC] a question about girafe

[Martin Morgan]

On 07/01/2011 08:01 PM, Sean Davis wrote:
> 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).

or Rsamtools asBam, sortBam, indexBam which are simple wrappers around 
samtools code so have the same basic memory / speed characteristics.

Martin

> 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
>>>>
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>>
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