[Bioc-sig-seq] Question about sbanBam() with AB SOLID data

James MacDonald jmacdon at med.umich.edu
Thu Nov 11 23:09:20 CET 2010

What aligner are you using that returns the sequences in color space? The SAM format specifies that:

"Color alignments are stored as normal nucleotide alignments with additional tags describing the raw color sequences, ..." 

So in general I wouldn't expect the seq to be color space, but nucleotide space. Depending on the aligner, you may get a CS:Z: tag of color space sequence, but I don't believe scanBam will parse that.



James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

>>> <ivan.borozan at utoronto.ca> wrote:
> Hello list,
> Can scanBam() be used with AB SOLID data (bam files) so that it can  
> return sequences in color space and with the right lengths?
> My read sequences are 50 bp in lengths however scanBam() is returning  
> sequences of length between 25 - 27 (they seem to be clipped) and  
> which are not in color space.
> Many thanks for any suggestions,
> Ivan
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