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i've got the same problem, just can not readcufflinks() correctly, and i wonder whether u solve the issue or not?
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Sorry，I haven't already solved the problems in cummeRbund packages. If there is any other way can address, please reply for me.
Thanks a lot.Comment
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Same issue: can't create the database using readCufflinks
I think this is something to do with the updated version, since it worked when I used the same files with a previous version, but with this version they don't work anymore.HTML Code:> cuff_data <- readCufflinks("diff_out_R", rebuild = TRUE) Creating database diff_out_R/cuffData.db Reading Run Info File diff_out_R/run.info Writing runInfo Table Reading Read Group Info diff_out_R/read_groups.info Writing replicates Table Reading Var Model Info diff_out_R/var_model.info Writing varModel Table Reading diff_out_R/genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch. In addition: There were 50 or more warnings (use warnings() to see the first 50)Comment
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Does anyone have a good solution for these errors? Mine looks like this:
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?Comment
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Hi jkofsky -
We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.
Hope it helps.Comment
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Thanks, I will follow the thread.Originally posted by Oskar View PostHi jkofsky -
We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.
Hope it helps.
I'm a little hesitant to assume its a bug considering data from cuffdiff (that was produced a year ago) is working fine ....Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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