[Bioc-sig-seq] pileup problem with converted Bowtie output

[joseph franklin]

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

joseph.franklin at yale.edu
407 341 3263 (cell)
203 654 7494 (google voice)