
Hi All

Does anyway know for sure the format of the quality scores in the fastq files generated by Rolexa. From what I can tell they are Phred33 but I would like to know for sure since bowtie needs to know the format of the quality scores. 

Thanks, 

Fuad

> quality(rs)
class: SFastqQuality
quality:
  A BStringSet instance of length 76069
        width seq
    [1]    32 hhehhgghhhhehgbhefghfNhTehg]^aeg
    [2]    18 ahVghdhfhhehhhZahh
    [3]    36 hhhhhhhhhhhhhhhhhhhhhhhhhhchhhghhhhh
    [4]    32 hhghhgh]Wb`^hhhbhhMh_dafc\gcffh_
    [5]    36 hhhhhhhhhhhhhhhhhhhhhUhhhhgghhhdhhTh
    [6]    31 hhhhhhghhhhhhhcXefhdhhhhOhhhhcg
    [7]    18 fTh^ghehhhhhedT\b[
    [8]    36 hhhhhhhhhhhhhhhhhhhhfhhhh^hhh]hh]dhg
    [9]    36 hhhhhhhhhhhhhhhhhhhghhghhghgbhhhbhhe
    ...   ... ...
[76061]    16 chdhZhe]hdPfdeha
[76062]    27 dhhhhhhdhhggfhhhchhRhehQhUf
[76063]    18 cgh`ghghh]hhhhfYRh
[76064]    16 ggf^d\hhaY[]ePdf
[76065]    18 ef]_gg`^fa^Q``dZ`a
[76066]    22 ehdaca`h^hhcThhghcZcgc
[76067]    16 `WgehghbgggeWggc
[76068]    20 hhchehfahUgMhabh[bhg
[76069]    29 chgaeehdgghhggc_dg`g\eXhffeN\

> 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] Rolexa_1.0.5       ShortRead_1.3.22   lattice_0.17-25    BSgenome_1.13.10  
[5] Biostrings_2.13.29 IRanges_1.3.44     mclust_3.3.1      

loaded via a namespace (and not attached):
[1] Biobase_2.4.1 grid_2.9.1    hwriter_1.1  


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