[Bioc-sig-seq] Problem with ShortRead reading quality scores from bowtie

[Martin Morgan]

Fuad Gwadry wrote:
> Hi All
> 
>  
> 
> I am getting negative values when reading quality scores when I read data generated in bowtie. Has anyone run into the same issue when using data generated by bowtie ? My session info is below. 

Hi Fuad -- ShortRead is reading the quality scores on the wrong scale 
(solexa, rather than phred; this will be fixed before the next release). Try

   qual <- FastqQuality(quality(quality(aln))
   initialize(aln, quality=qual)

to update aln, or

   m <- as(FastqQuality(quality(quality(aln)), "matrix")

for a one-off solution.

Martin

> 
>  
> 
> Thanks in advance
> 
>  
> 
> Fuad
> 
>  
> 
>> aln
> class: AlignedRead
> length: 4591807 reads; width: 32 cycles
> chromosome: chr13 chr7 ... chr6 chr4 
> position: 93437004 13223395 ... 23636747 23353864 
> strand: - - ... + + 
> alignQuality: NumericQuality 
> alignData varLabels: similar mismatch 
> 
> 
>> m <- as(quality(aln), "matrix")
>> colMeans(m)
>  [1]  -7.186638  -7.205858  -7.203382  -7.197175  -7.203629  -7.217016
>  [7]  -7.240661  -7.249238  -7.268499  -7.286551  -7.306615  -7.324003
> [13]  -7.523238  -7.581242  -7.697591  -7.695861  -7.735321  -7.743323
> [19]  -7.752996  -7.849403  -7.862658  -7.931969  -7.979778  -8.029288
> [25]  -8.120469  -8.215818  -8.335176  -8.411609  -8.587005  -8.820979
> [31] -11.447326 -11.644198
> 
> 
>> sessionInfo()
> R version 2.9.1 (2009-06-26) 
> x86_64-unknown-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] ShortRead_1.3.22   lattice_0.17-25    BSgenome_1.13.10   Biostrings_2.13.29
> [5] IRanges_1.3.44    
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.1 grid_2.9.1    hwriter_1.1  
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793