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

joseph franklin joseph.franklin at yale.edu
Wed Mar 25 12:38:23 CET 2009


Martin,
Thanks for the tip--works great.
-joe

On 24 Mar 2009, at 17:19, Martin Morgan wrote:

> 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)
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
> -- 
> 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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