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

Newsbot! · 09-10-2011, 03:12 AM

Syndicated from PubMed RSS Feeds

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 · 09-15-2011, 09:27 AM

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

Chrevan · 10-10-2011, 06:17 PM

Quote:

Originally Posted by mosalem

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

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

byou678 · 10-14-2011, 08:33 AM

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 · 11-01-2011, 10:34 AM

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

Alexandre Cormier · 02-06-2012, 05:15 AM

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

kopi-o · 02-06-2012, 05:55 AM

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 ...

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09-10-2011, 03:12 AM	#1
Newsbot! RSS Posting Maniac Join Date: Feb 2008 Posts: 1,443	RNA-Seq: DEB: A web interface for RNA-seq digital gene expression analysis. Syndicated from PubMed RSS Feeds 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] More...

09-15-2011, 09:27 AM	#2
mosalem Junior Member Location: US Join Date: Sep 2011 Posts: 3	I have tried it, no results after >3 days.

10-14-2011, 08:33 AM	#4
byou678 Member Location: Maryland Join Date: Aug 2011 Posts: 52	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.

11-01-2011, 10:34 AM	#5
allenma Junior Member Location: Boulder, Co Join Date: Mar 2011 Posts: 5	Using there Demo file works. But no luck with my file. Just tries forever and no error message.

02-06-2012, 05:15 AM	#6
Alexandre Cormier Junior Member Location: France Join Date: Apr 2011 Posts: 1	Same problem, demo files work, but impossible to get results with my data. Someone had a DEB answer?

02-06-2012, 05:55 AM	#7
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	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 ...