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

[ivan.borozan at utoronto.ca]

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.

Best,

Ivan

Quoting James MacDonald <jmacdon at med.umich.edu>:

> 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
>
>
>>>> <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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