cummeRbund problem in creating database
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Entering edit mode
@majeedaasim-14248
Last seen 4.9 years ago

I ran cummRbund on cuffdiff output directory. Following error is depicted.

 

library(cummeRbund)

getwd()
setwd("E:/AASIM/tx_win_cummeRbund/tx_win_cuffdiff_output/")
list.files()

 [1] "bias_params.info"               "cds.count_tracking"             "cds.diff"                      
 [4] "cds.fpkm_tracking"              "cds.read_group_tracking"        "cds_exp.diff"                  
 [7] "cuffData.db"                    "gene_exp.diff"                  "genes.count_tracking"          
[10] "genes.fpkm_tracking"            "genes.read_group_tracking"      "isoform_exp.diff"              
[13] "isoforms.count_tracking"        "isoforms.fpkm_tracking"         "isoforms.read_group_tracking"  
[16] "promoters.diff"                 "read_groups.info"               "run.info"                      
[19] "splicing.diff"                  "SuperDuper.fasta.fasta"         "transcripts.gtf"               
[22] "tss_group_exp.diff"             "tss_groups.count_tracking"      "tss_groups.fpkm_tracking"      
[25] "tss_groups.read_group_tracking" "var_model.info"  

cuff= readCufflinks(dbFile = "cuffData.db",dir = "tx_win_cuffdiff_output/", gtfFile = "transcripts.gtf",

+                     genome = "SuperDuper.fasta.fasta", rebuild = T)

Creating database tx_win_cuffdiff_output//cuffData.db

Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) : 

  Could not connect to database:

unable to open database file

> cuff

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

Where did I err?

cummerbund data run error • 708 views
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Entering edit mode

Since the update of some of the SQL R pacakages cummeRbund have had quite a few problems. Try updating to the latest version from the devel branch (by typing "useDevel()" before installing). 

If it still does not work remember to repport the output from sessionInfo().

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