Fuad Gwadry wrote:
Hi Martin
I followed the same steps using the data from a newer version of the
illumina pipeline (ver 1.3). Still run into the same issues.
Fuad
##########################
original data illumina 1.3
#########################
> alignQuality(aln)
class: NumericQuality
quality: NA NA ... NA NA (4585850 total)
> head(quality(aln))
class: SFastqQuality
quality:
A BStringSet instance of length 6
width seq
[1] 35 ;;;;;;;;;;;;;;;;;;;;;;;;;;:;;;57547
[2] 35 ;:7;;;;;;7;;;;4;;;;;:;:7;77;;;5+444
[3] 35 ;;:;;;:::;;;:;:;;9:6;;;9:;;:;972479
[4] 35 ;;6;;;;;;;;;;:;;;;;;9&9;;;;9;;99587
[5] 35 ;;;;:9;;;;:;;79;;;/::;66;)7;4/78487
[6] 35 ;-;;;;;;;;;;;;;;;;;8;;;;;;;;;055-75
> m <- as(quality(aln), "matrix")
> colMeans(m)
[1] -6.044744 -5.936636 -5.924813 -5.958905 -5.956505 -5.921455
[7] -5.929669 -5.967875 -5.929279 -5.970600 -5.975925 -6.011533
[13] -6.462944 -6.520501 -6.601669 -6.651007 -6.805869 -6.832879
[19] -6.874413 -7.030044 -7.153979 -7.210835 -7.278909 -7.363969
[25] -7.475453 -7.662229 -7.781669 -7.915972 -8.113778 -8.222790
[31] -12.165080 -12.329542 -12.456710 -12.590711 -12.737429
##########################
incorporated your suggestions
##########################
> qual <- FastqQuality(quality(quality(aln)))
> qual
class: FastqQuality
quality:
A BStringSet instance of length 4585850
width seq
[1] 35 ;;;;;;;;;;;;;;;;;;;;;;;;;;:;;;57547
[2] 35 ;:7;;;;;;7;;;;4;;;;;:;:7;77;;;5+444
[3] 35 ;;:;;;:::;;;:;:;;9:6;;;9:;;:;972479
[4] 35 ;;6;;;;;;;;;;:;;;;;;9&9;;;;9;;99587
[5] 35 ;;;;:9;;;;:;;79;;;/::;66;)7;4/78487
[6] 35 ;-;;;;;;;;;;;;;;;;;8;;;;;;;;;055-75
[7] 35 ;:9;;;;;;;;;;;;;:;:;;;;:;;;;+:54455
[8] 35 ;;;;;;:;;;:;;;;;:;;3:9;;;;:;;;45544
[9] 35 ;;:;;;;;;;4;;;4;:7;:;;;74;;;;644015
... ... ...
[4585842] 35 0:;7;;-;;;;;:;;7)-.25;;&;;9;7;.4444
[4585843] 35 7477:.-;9*;3;0979489.-9::&;49:5-344
[4585844] 35 6:;::;;;;;:;:;;6::98:3962:949:24424
[4585845] 35 0:;;:::6;::.:::626:277:8)9::7:)5--0
[4585846] 35 4;7+9-;;;;6:;);9;+2037:&0-270&4.-1.
[4585847] 35 :;;::;;;;;;;0;:96.:9:9;2;);99;54544
[4585848] 35 ;;:9;:;;;;:;:7,0)9;);))9.;6:4;4245-
[4585849] 35 8:;;;;;:668:;2;:,836:;69:993::454,0
[4585850] 35 889;:;;;;;;-;-.89);;;);;4044*7*4.41
> initialize(aln, quality=qual)
class: AlignedRead
length: 4585850 reads; width: 35 cycles
chromosome: shank3genomic shank3genomic ... shank3genomic shank3genomic
position: 37625 19915 ... 13278 39832
strand: + + ... + +
alignQuality: NumericQuality
alignData varLabels: similar mismatch
> m <- as(quality(aln), "matrix")
> colMeans(m)
[1] -6.044744 -5.936636 -5.924813 -5.958905 -5.956505 -5.921455
[7] -5.929669 -5.967875 -5.929279 -5.970600 -5.975925 -6.011533
[13] -6.462944 -6.520501 -6.601669 -6.651007 -6.805869 -6.832879
[19] -6.874413 -7.030044 -7.153979 -7.210835 -7.278909 -7.363969
[25] -7.475453 -7.662229 -7.781669 -7.915972 -8.113778 -8.222790
[31] -12.165080 -12.329542 -12.456710 -12.590711 -12.737429
> alignQuality(aln)
class: NumericQuality
quality: NA NA ... NA NA (4585850 total)
###############################
Also tried your second suggestion and ended up with teh following error
##############################
> m <- as(FastqQuality(quality(quality(aln)), "matrix"))
Hi Faud --
here the problem is a mis-placed parenthesis -- check out "matrix" in
as(FastqQuality(quality(quality(aln))), "matrix")
I see that I was missing a ) in my original reply, so sorry about that.
Martin
Error in .identC(Class, "double") :
element 2 is empty;
the part of the args list of '.Call' being evaluated was:
("R_identC", c1, c2, PACKAGE = "methods")
> 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
------------------------------------------------------------------------
Attention all humans. We are your photos. Free us.
<http://go.microsoft.com/?linkid=9666046>
--
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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