Hi,
I have a seemingly simple problem with pileups computed from Bowtie
output. I'm trying to use Bioconductor 2.3, which means I have to
convert from Bowtie to MaqMap to MaqMapview (I get an error using
either type="MaqMap" or "MaqMapShort" when applying readAligned to the
output of the bowtie-maqconvert tool).
As you can see below, it appears that I have too many levels ( "-" "+"
"*") in the strand vector of my aligned reads object "set". If anyone
has any suggestions on how to fix this in 2.3 (I realize that 2.4
allows direct import of Bowtie), or further diagnose the problem,
please let me know.
thanks-
joe
>set <- readAligned(folder, type="MAQMapview")
> pup <- pileup(position(set[chromosome(set)==chr]), width(set1),
lens[[chr]], dir=(strand(set[chromosome(set)==chr])))
Error: length(levels(dir)) == 2 && all(levels(dir) == c("-", "+")) is
not TRUE
> length(strand(set[chromosome(set)==chr]))
[1] 282941
> length(position(set[chromosome(set)==chr]))
[1] 282941
> levels(strand(set[chromosome(set)==chr]))
[1] "-" "+" "*"
> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-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] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ShortRead_1.0.7 lattice_0.17-20 Biobase_2.2.2
Biostrings_2.10.21
[5] IRanges_1.0.14
loaded via a namespace (and not attached):
[1] grid_2.8.1 Matrix_0.999375-17
________________________________
Joe Franklin
Department of Cell Biology
Yale University School of Medicine
295 Congress Ave, BCMM 137
New Haven, CT 06519
USA
[email protected]
407 341 3263 (cell)
203 654 7494 (google voice)
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