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?
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: