Hello list,

 

I would like to use Biostrings to work with A. thaliana genome sequence. But, when I tried to extract the sequence from BSgenome.Athaliana.TAIR.01222004 library I've got the following errors. Does anyone know why this happen and how I can solve it?

 

> library("Biostrings", lib.loc="/common/users/dreosr/unix/software/lib")

> library("BSgenome", lib.loc="/common/users/dreosr/unix/software/lib")

> library("BSgenome.Athaliana.TAIR.01222004", lib.loc="/common/users/dreosr/unix/software/lib")

> Athaliana$chr1

Error in readChar(con, 5) : cannot open the connection

In addition: Warning message:

In readChar(con, 5) :

  cannot open compressed file '', probable reason 'No such file or directory'

> Athaliana[[chr1]]

Error in readChar(con, 5) : cannot open the connection

In addition: Warning message:

In readChar(con, 5) :

  cannot open compressed file '', probable reason 'No such file or directory'

 

> sessionInfo()

R version 2.6.2 (2008-02-08) 

x86_64-redhat-linux-gnu 

 

locale:

LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

 

attached base packages:

 [1] grid      splines   tools     stats     graphics  grDevices utils    

 [8] datasets  methods   base     

 

other attached packages:

 [1] BSgenome.Athaliana.TAIR.01222004_1.3.1

 [2] BSgenome_1.6.2                        

 [3] Biostrings_2.6.6                      

 [4] WiggeNorm_1.0                         

 [5] quantsmooth_1.4.0                     

 [6] quantreg_4.17                         

 [7] SparseM_0.75                          

 [8] lodplot_1.1                           

 [9] gcrma_2.10.0                          

[10] matchprobes_1.10.0                    

[11] affxparser_1.10.2                     

[12] affy_1.16.0                           

[13] preprocessCore_1.0.0                  

[14] affyio_1.6.1                          

[15] Biobase_1.16.3

 

Thank you

René

 


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