
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. 

 

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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