RNA-Seq: DEB: A web interface for RNA-seq digital gene expression analysis.

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DEB: A web interface for RNA-seq digital gene expression analysis.

Bioinformation. 2011;7(1):44-5

Authors: Yao JQ, Yu F

Abstract
Digital expression (DE) is an important application of RNA-seq technology to quantify the transcriptome. The number of mapped reads to each transcript or gene varies under different conditions and replicates. Currently, three different statistical algorithms (edgeR, DESeq and bayseq) are available as R packages, to compare the reads to identify significantly expressed transcripts or genes. So far, users have to manually install and run each R package separately. It is also of users' interest to compare the results of different approaches. Here, we present a pipeline DEB which automates all the steps in file preparation, computation and result comparison. AVAILABILITY: The database is available for free at http://www.ijbcb.org/DEB/php/onlinetool.php.


PMID: 21904439 [PubMed - in process]



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[mosalem]

I have tried it, no results after >3 days.

[Chrevan]

I have tried it, no results after >3 days.

Me too, it takes such a long time or there is no result!

[byou678]

I am in the same boat. It takes a very long time for relatively large data/file. But using only the first 60 genes of the example/demo data, i get the result after about 3 mins (choose only one algorithm). Could the authors or anybody give us some ideas or solutions? Thanks.

[allenma]

Using there Demo file works. But no luck with my file. Just tries forever and no error message.

[Alexandre Cormier]

Same problem, demo files work, but impossible to get results with my data. Someone had a DEB answer?

[kopi-o]

No, I've tried it several times and it has never worked. Actually just writing an R script that calls edgeR, baySeq and DESeq takes about 10 minutes if you follow the respective vignettes, so I've realized this web interface is rather pointless ...