[Bioc-sig-seq] short read quality score summary in ShortRead error

[Martin Morgan]

On 02/01/2011 11:08 AM, Kunbin Qu wrote:
> Hi, all:
> 
> I am trying to assess the read quality score for each lane (mean and
median etc.) from a Hi-Seq run which has about 70-90 million reads per
lane. When I used as(quality(readFastQ), "numeric"), it gave an error
"allocMatrix: too many elements specified". Is there a way to get around
this? Thanks.

An R vector (including a matrix) must be less than 2^31-1 elements long,
so a work-around is to divide the ShortReadQ object into chunks such
that sum(width(s1q)) < 2^31-1.

Depending on what you do down-stream, it might be sufficient to use
alphabetByCycle (alphabet use epr cycle) or alphabetFrequency (alphabet
use per read).

Martin

> 
> -Kunbin>
> 
>> seqQ
> class: ShortReadQ
> length: 76115764 reads; width: 50 cycles
>> s1q<-quality(seqQ)
>> s1q
> class: SFastqQuality
> quality:
>   A BStringSet instance of length 76115764
>            width seq
>        [1]    50 aa``_BcccccccccddddddadJdQTTTB]]SZY[\_PZbc_bbddad\
>        [2]    50 ]\SUTB_[[][]]]]dfecfef^cddffcedbd^ddeed`cd`dedeef`
>        [3]    50 aa```Bcccb\ccccggggggggegegefgggege^abbdeeabedgade
>        [4]    50 ^VZXWB_YN]TMUTYddadd_dcda[[R[T\``Wc^bc\bacaddd`a\d
>        [5]    50 cccccBc]cacbb]cgggdfggegegaggeeggggaeegggbecgefcZ\
>        [6]    50 ddccdbeeea_]]`Z\cc`c]SZ_]]S[K]ccbbWaTL_``V]^_cddWV
>        [7]    50 XYWWYB[]_]]]^\]cddddbfedfdddbacacacfff_edTd`aU[XYX
>        [8]    50 bbb`bBcccccddddgggggggggggegggfggdgggggegeggdggggg
>        [9]    50 bba`bBcccccddddgeggegggggdggffggcfe`edeegae`geddd`
>        ...   ... ...
> [76115756]    50 e`eeeBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115757]    50 aaVa`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115758]    50 ]ZXRERHZZFUZ[XDKKDDRHLPUQa```^XZ^HQ`]]T[WDXRH^YSWW
> [76115759]    50 eeededd_dcBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115760]    50 c[^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115761]    50 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115762]    50 __BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115763]    50 _^X_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> [76115764]    50 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
>> summary(as(s1q, "numeric"))
> Error in asMethod(object) : allocMatrix: too many elements specified
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] 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_1.6.2     Rsamtools_1.0.1     lattice_0.19-11
> [4] Biostrings_2.16.7   GenomicRanges_1.0.1 IRanges_1.6.8
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.3   tools_2.11.0
>>
> 
> 
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