[BioC] a question about girafe

[Sean Davis]

On Tue, Jul 5, 2011 at 11:11 AM, chun-jiang he <camelbbs at gmail.com> wrote:
> 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

Looks like you specified type="Bowtie".  You have a bam file, not a
bowtie-formatted file.  Have a look at the help for readAligned() to
get a list of available types.

Sean


> Jiang
> On Sun, Jul 3, 2011 at 7:09 AM, Martin Morgan <mtmorgan at 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 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
>>>>>>
>>>>>>        [[alternative HTML version deleted]]
>>>>>>
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>>>>>
>>>>
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>>>>
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>>
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>>
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>
>