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

[Martin Morgan]

Hi joe --

joseph franklin <joseph.franklin at yale.edu> 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
>
> joseph.franklin at yale.edu
> 407 341 3263 (cell)
> 203 654 7494 (google voice)
>
> _______________________________________________
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> Bioc-sig-sequencing at r-project.org
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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