Martin,
Thanks for the tip--works great.
-joe
On 24 Mar 2009, at 17:19, Martin Morgan wrote:
Hi joe --
joseph franklin <[email protected]> writes:
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.
as a work-around, convert your strand(set[chromosome(set)==chr]) to a
new factor with the levels pileup wants,
factor(as.character(strand(set[chromosome(set)==chr])),
levels=c("-", "+"))
Martin
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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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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