Question: Error in CummeRbund
0
gravatar for majeedaasim
2.7 years ago by
majeedaasim40
United States
majeedaasim40 wrote:

I try to run CummeRbund on output generated by cuffdiff i.e. tx_win_cuffdiff_output. I just put it in a directory and the made this a working directory. How I am not able to generate SQLite database. I used the following commands: My machine details are

R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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" "transcripts.gtf"
[22] "tss_group_exp.diff" "tss_groups.count_tracking" "tss_groups.fpk _tracking"
[25] "tss_groups.read_group_tracking" "var_model.info"cuff= read

 cuff= read Cufflinks(dbFile = "cuffData.db",dir = "tx_win_cuffdiff_output/", gtfFile = "transcripts.gtf" genome = "SuperDuper.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

Why is not SQLite database produced in my case? What I have to do?

cummerbund R • 1.0k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by majeedaasim40

Is it an issue with just the current working directory?

When it is "Creating database tx_win_cuffdiff_output//cuffData.db", I think that the file that it's aiming to create is: E:/AASIM/tx_win_cummeRbund/tx_win_cuffdiff_output/tx_win_cuffdiff_output//cuffData.db, i.e., tx_win_cuffdiff_output, is there twice.

Change the working directory to E:/AASIM/tx_win_cummeRbund/ and then execute:

cuff= read Cufflinks(dbFile = "cuffData.db",dir = "tx_win_cuffdiff_output", gtfFile = "tx_win_cuffdiff_output/transcripts.gtf" genome = "tx_win_cuffdiff_output/SuperDuper.fasta", rebuild = T)
ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Kevin Blighe61k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1509 users visited in the last hour