Hello everyone,
  I am trying to do some quality trimming on some RNA seq reads (Illumina,
100 bp, single end).  I have been following the pipeline from the UCR
manuals<http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Trimming-Low-Quality-3-Tails-from-R>
but
I have run into an error I can't seem to resolve.

library(ShortRead)
reads <- readFastq("myFile.fastq")

qualityCutoff <- 10 # remove read tails with quality lower than this

seqs <- sread(reads) # get sequence list

qual <- PhredQuality(quality(quality(reads))) # get quality score list as
PhredQuality

> length(qual)                 #my length is positive
[1] 39145018

> myqual_mat <- matrix(charToRaw(as.character(unlist(qual))),
nrow=length(qual), byrow=TRUE)
Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
  negative length vectors are not allowed

as(qual, matrix) gives the same error, and as.matrix(qual) does as well,
not sure how those two commands are different, but tried anyway.

If I run the exact same commands, instead of the full 39145018 reads, I use
the first 100, it works like a charm.  I am working on a linux cluster, if
that is important

Does anyone have an idea?

Cheers!
-- 
Sam McInturf

A look at my data:

> seqs
  A DNAStringSet instance of length 39145018
           width seq
       [1]   100
ATCNCAAAGGTATATTTTGAATCAAAAACA...TTCTTTTTCTGGACCTTGAGGGAAAGGGGG
       [2]   100
CGANCTTGACCGTTGAGAAATTATCAGCTG...AGCTTCAGTCAATTCCACACAGTCTGAAAA
       [3]   100
GATNGTAGGACGGAAAAAGAATNNNNNGTT...GAAANNNGTTGGTCACAACTGTTANNCACC
       [4]   100
GCAACGTTATCGGCGATCGCACTGAAGACG...CCAGAGTTCTCCTCCCACTGATCGTCCTGT
       [5]   100
GACGATTAAAGGAGCTTATGAGGACTCTTT...TTGTTTGATAGGATTATTCAGAGAGGACAT
       ...   ... ...
[39145014]   100
ACAAGGGATAAAATCAAAGATGGGTGATAA...TGAAGCTTGGTGGCTTGTAGGCAATGAAAC
[39145015]   100
CATGCTTCTCCTTCTCTTTTTCTTTGTGTC...TTGTTCTCCTCCTCAACATCTCTCTCCCTC
[39145016]   100
CAGCGACTATCAGTGTAAACTCCAATCTTG...CTGGCCGTACCAATCCAACCGCATGCTTCA
[39145017]   100
CGTGCGTGGGATGTTTCCGGTGAGGCGTGG...CCGATCCGGTACGAGATCTCACCGCAGACT
[39145018]   100
TACTTGAGGAAATGGTGTTTAGTTGCTGTG...AGCCTCAAGTTCCACGTTACTTCATCTTTG

> qual
  A PhredQuality instance of length 39145018
           width seq
       [1]   100
@@@#4=D?DD<DHGIIIIDHHIIIIIIGHH...=?############################
       [2]   100 @@@#4==A??DHH?BBBBCEGHCHGIIIII...@=AEEAC@??CBCECE@
>;?1=5>CCC@C3
       [3]   100
##############################...##############################
       [4]   100 @@CADDFDFHFGGIIIIIIG=GEIIEGHIH...ACCCA?>>:>A>:<C?<A<A:C@
?<<?###
       [5]   100 C@BFFFFFHGHHHIIIJJJJJJJJIIJJJI.
..GIIGHEHHHHFFFFFFCEEDEEEDDDDBDD
       ...   ... ...
[39145014]   100
@@@=?ADD>CFFFBFIIBHIIHF<??CACF...<BCCC:;(5;5=5<<?',:55:A?######
[39145015]   100
##############################...##############################
[39145016]   100
?@<+=ADDFFHGHHGEFHIIIIGG+<CHGI...FFE>=A??DD<CCDCDDDCBBBD3?:@A@C
[39145017]   100 ?=:+==2@<CDDDE@BEIDA
##########...##############################
[39145018]   100
(;<38>)<7>@>8=:)2:-=@;)9)=9?.2...##############################

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ShortRead_1.18.0     latticeExtra_0.6-24  RColorBrewer_1.0-5
[4] Rsamtools_1.12.3     lattice_0.20-15      Biostrings_2.28.0
[7] GenomicRanges_1.12.3 IRanges_1.18.1       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] Biobase_2.20.0 bitops_1.0-5   grid_3.0.0     hwriter_1.3
 stats4_3.0.0
[6] zlibbioc_1.6.0

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