On 11/11/2010 02:25 PM, [email protected] wrote: > Bioscope pipeline was used to align the data. In order to get reads in > color space and their quality > > param<- ScanBamParam(tag=c("CQ")) > > and > > param<- ScanBamParam(tag=c("CS")) > > > should be specified.
Hi Ivan -- I'm a little confused about where this leaves you. Can you actually read the sequences / quality strings in to R? Are they represented in sequence space? Is there a BAM file available somewhere to experiment with? Martin > > Best, > > Ivan > > Quoting James MacDonald <[email protected]>: > >> 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 >> >> > > > > > > > > ----- End forwarded message ----- > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
