Hi Martin,
I was able to read the sequences in color space into R together with
the quality scores - they are not represented in sequence space (we
needed color space info). Unfortunatly I do not have a bam file that I
could point to.
Ivan
Quoting Martin Morgan <[email protected]>:
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
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