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
_________________________________________________________________
[[alternative HTML version deleted]]
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
