Martin Morgan wrote:
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.
I wanted to clarify, too, both for this post and one yesterday, that
as() is simply converting the character encoding to the corresponding
integer value that each letter encodes; there is a secondary mapping
from this encoding to log-odds or phred score that is not being
performed. This step is, I think
10^(-m/10) for phred scores
1 - 1 / (1 + 10^(-m/10)) for Solexa scores
Solexa has changed its encoding scheme very recently; I think it is now
standard phred but am not sure.
Martin
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
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