cummeRbund error when loading cuffdiff data output

Question

[jkofsky]

Hi, I am having an issue loading my cuffdiff output into cummeRbund. The follow are the errors I receive:

Creating database /cuffData.db Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) : Could not connect to database: unable to open database file

or 50+ of these:

1: In rsqlite_fetch(res@ptr, n = n) : Don't need to call dbFetch() for statements, only for queries

depending on how I submit it

From what I've read people have solved these issues by altering with the input (no symbols in the table) or by correcting the working directory. I have tried these and everything else I can think of. I have tried a cuffdiff output from a previous version and experiment and it runs in cummerbund fine...

I'm stuck. does anyone have a suggestion?

Answer 1

[bhagyathimmappa]

Hola,

I have some issues, I do not get any error but database gives me zero samples, zero genes...what is wrong? can someone please help me.

cuff_data <- readCufflinks('diff_out_BMG/')
cuff_data
CuffSet instance with:
     0 samples
     0 genes
     0 isoforms
     0 TSS
     0 CDS
     0 promoters
     0 splicing
     0 relCDS
cuff_data
CuffSet instance with:
     0 samples
     0 genes
     0 isoforms
     0 TSS
     0 CDS
     0 promoters
     0 splicing
     0 relCDS

Thanks.

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

It doesn't look like there is a connection between your question and the original question in this thread, if so it would be more appropriate to open a separate thread for your question.

You should also know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using kallisto or salmon.