[Bioc-devel] accessing gapped alignment

Daniel.Berner at unibas.ch Daniel.Berner at unibas.ch
Mon Dec 20 14:27:04 CET 2010

dear developers
I have performed a gapped alignment of my illumina reads. I now want  
to analyze the output by accessing the CHROMOSOME and POSITION  
information contained in the BAM file. I therefore uploaded the BAM  
using readAligned(), but found that
all those reads aligning to the reference genome with a GAP are  
missing. However, when using readGappedAlignments(), I loose  
information crucial to my analysis (i.e., chromosome, position). Is  
there any way to upload into R GAPPED
alignments while preserving read ID, chromosome, position etc?
Daniel Berner

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