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

ivan.borozan at utoronto.ca ivan.borozan at utoronto.ca
Mon Nov 15 19:51:41 CET 2010


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 <mtmorgan at fhcrc.org>:

> On 11/11/2010 02:25 PM, ivan.borozan at utoronto.ca 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 <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
>>>>
>>>> _______________________________________________
>>>> Bioc-sig-sequencing mailing list
>>>> Bioc-sig-sequencing at r-project.org
>>>> 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
>> Bioc-sig-sequencing at r-project.org
>> 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
>



More information about the Bioc-sig-sequencing mailing list