CummeRbund error can't make database from Cuffdiff data

Richard Barker

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Join Date: Apr 2012

Posts: 47
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CummeRbund error can't make database from Cuffdiff data

08-15-2012, 09:11 AM

Hello.
I can't fill cummeRbund databases in R (running on ubuntu), it appears to create the data base (the file is 41Kb) but then errors when its tries to process/load the first file (see below), i assume this should then subsequently load all the other data after (eg. cds, isoforms, tss in either/both FPKM, diff and count tracking etc..). I'm writing the following script in the directory containg the cuffdiff out puts.
Any ideas gratefully received...

/home/richard/RNA_seq_analysis/run296_cuffdiff/cuffdiff_0$ R
...
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
loading text info etc...
...
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> cuff_data_0 <- readCufflinks()
Creating database /home/richard/RNA_seq_analysis/run296_cuffdiff/cuffdiff_0/cuffData.db
Reading /home/richard/RNA_seq_analysis/run296_cuffdiff/cuffdiff_0/genes.fpkm_tracking
Error in function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", :
no lines available in input

Last edited by Richard Barker; 08-15-2012, 09:13 AM. Reason: typo
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Richard Barker

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Join Date: Apr 2012

Posts: 47
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#2

08-15-2012, 10:11 AM

Could this be caused by installing a newer version of cufflinks? I think i used an older version for the transcript reconstruction and have installed the latest version which is now being used by R and cummeRbund. Is there anyway to select the older version of cufflinks to test this theory?
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CummeRbund error can't make database from Cuffdiff data

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