Question: Unable to load sqlite file generated by Cuffdiff
gravatar for handgabriel
21 days ago by
handgabriel0 wrote:

I am trying to perform read counts with summarizeOverlaps using the following code, using an sqlite file generated with Cuffdiff:

library("GenomicFeatures"); library(BiocParallel)
txdb <- loadDb("./data/PR0735.galaxy.sqlite")
eByg <- exonsBy(txdb, by=c("gene"))
bfl <- BamFileList(outpaths(args), yieldSize=50000, index=character())
multicoreParam <- MulticoreParam(workers=4); register(multicoreParam); registered()
counteByg <- bplapply(bfl, function(x) summarizeOverlaps(eByg, x, mode="Union",
countDFeByg <- sapply(seq(along=counteByg), function(x) assays(counteByg[[x]])$counts)
rownames(countDFeByg) <- names(rowRanges(counteByg[[1]])); colnames(countDFeByg) <- names(bfl)
rpkmDFeByg <- apply(countDFeByg, 2, function(x) returnRPKM(counts=x, ranges=eByg))
write.table(countDFeByg, "results/countDFeByg.xls", col.names=NA, quote=FALSE, sep="\t")
write.table(rpkmDFeByg, "results/rpkmDFeByg.xls", col.names=NA, quote=FALSE, sep="\t")

but when I run txdb <- loadDb("./data/PR0735.galaxy.sqlite") I get the following error:

Error: dbExistsTable(conn, "metadata") is not TRUE
Can anyone help with this error? I have not been able to find any information online at all.
ADD COMMENTlink written 21 days ago by handgabriel0

The `loadDb` function is meant to load `txdb` objects. The sqlite file from cuffdiff is, indeed, a sqlite file, but it does not contain the same information as a `txdb` object. So, I do not think that your code should be expected to work. 

ADD REPLYlink written 21 days ago by Sean Davis21k

Thanks for your help. It's worth noting that code comes from the systemPipeR RNASeq workflow vignette so perhaps I should contact the author?

ADD REPLYlink written 19 days ago by handgabriel0
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