Entering edit mode
Zhenyu Xu
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10
@zhenyu-xu-5556
Last seen 9.6 years ago
Hi ShortRead package developer,
I tried to use the function trimTails to trim some bad quality
bases from reads coming out of 454 sequencing machine. However I got
different results if I run the command several times starting from the
same ShortReadQ object and same trimming parameter. This is observed
in centos linux machine (6.2 and 6.3). I also tried this with my own
mac machine, but the results are identical. So seems the problem only
restrict to centos linux machine (Not sure other linux platform has
this problem or not). the data sets(~11Mb) can be downloaded at
http://dl.dropbox.com/u/68829208/454reads.rds.
best,
zhenyu
Please see the following of the execution:
wget http://dl.dropbox.com/u/68829208/454reads.rds
R
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
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ISBN 3-900051-07-0
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> library(ShortRead)
Loading required package: BiocGenerics
Attaching package: ?BiocGenerics?
The following object(s) are masked from ?package:stats?:
xtabs
The following object(s) are masked from ?package:base?:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
> readsSub <- readRDS("454reads.rds")
> readsSub
class: ShortReadQ
length: 5460 reads; width: 5..424 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 3..416 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 3..416 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 4..424 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 5..416 cycles
> trimTails(readsSub, 20, "5", successive=TRUE)
class: ShortReadQ
length: 5460 reads; width: 4..424 cycles
> x = trimTails(readsSub, 20, "5", successive=TRUE)
> y = trimTails(readsSub, 20, "5", successive=TRUE)
> sum(width(x)!=width(y))
[1] 1325
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.14.4 latticeExtra_0.6-19 RColorBrewer_1.0-5
[4] Rsamtools_1.8.5 lattice_0.20-6 Biostrings_2.24.1
[7] GenomicRanges_1.8.9 IRanges_1.14.4 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.1 hwriter_1.3
stats4_2.15.1
[6] zlibbioc_1.2.0
