[BioC] a question about girafe

Joern Toedling j.toedling at imb-mainz.de
Wed Jul 6 09:39:56 CEST 2011


note that package "girafe" also contains a function called "agiFromBam" 
which directly reads in sorted and indexed BAM files into an object of 
the AlignedGenomeIntervals class. This function also relies on 
functionalities of the Rsamtools package but should be faster and more 
memory-efficient than first using "readAligned" and then converting the 
result into an AlignedGenomeIntervals object. Please let me know if 
there are any issues with that function.


On 07/05/2011 05:36 PM, Sean Davis wrote:
> 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

Joern Toedling, PhD
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
Tel.: +49 6131 39 21511

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