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. Best, Jim -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 >>> <[email protected]> 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
