Hi,

Thanks. There is an error when I run readAligned(). I have converted .sam to
.bam and sorted indexed it. I got two files as sorted.bam and sorted.bam.bai

> exA<-readAligned(dirPath="~",type="Bowtie",
+ pattern="SRR032476-sorted.bam")
Error: Input/Output
  'readAligned' failed to parse files
  dirPath: '~'
  pattern: 'SRR032476-sorted.bam'
  type: 'Bowtie'
  error: incorrect number of fields (1) /cchome/che/SRR032476-sorted.bam:1

Jiang

On Sun, Jul 3, 2011 at 7:09 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 07/01/2011 08:01 PM, Sean Davis wrote:
>
>> On Fri, Jul 1, 2011 at 10:55 PM, chun-jiang he<camelbbs@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@mail.nih.gov>  wrote:
>>>
>>>  On Fri, Jul 1, 2011 at 6:14 PM, chun-jiang he<camelbbs@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<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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