Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNAseq: Pipeline to detect allele specific expression dariober Bioinformatics 9 07-17-2015 12:46 PM
plant annotation pipeline for assembled RNAseq? vebaev RNA Sequencing 27 08-19-2014 12:43 AM
Pipeline + test datset for RNAseq with ERCC controls? danwiththeplan RNA Sequencing 0 03-10-2013 01:58 PM
Total RNAseq and cufflinks/cuffmerge/cuffdiff/cummeRbund pipeline JWC Bioinformatics 8 08-01-2012 05:41 AM
What is the best pipeline for RNASeq atm? foxyg Bioinformatics 6 09-02-2010 07:56 PM

Thread Tools
Old 09-01-2015, 07:46 AM   #1
Location: USA

Join Date: Jun 2011
Posts: 44
Default How to validate RNAseq pipeline

I have created a pipeline to process RNAseq data and have used DEseq to conduct differential expression analysis. The question is, how do I know it is giving valid results? Are there any gold standard datasets with which I can compare my results?
biofreak is offline   Reply With Quote
Old 09-03-2015, 02:26 AM   #2
Location: Germany

Join Date: Jan 2014
Posts: 39

One possibility would be the Flux simulator, which is simulating RNA-Seq experiments. In the .pro file you can see the actual amount of transcripts in your transcriptome, the number of produced fragments from the transcripts as well as the number of reads produced from each transcript. You could then analyze the simulated fastq-file with your pipeline and compare your findings to the values in the .pro file.
Mchicken is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:00 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO