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Old 01-09-2012, 09:58 AM   #1
hmortens
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Location: RTP

Join Date: Aug 2011
Posts: 12
Default tophat/Cufflinks workflow question

I am still trying to make sure that I am running tophat/cufflinks in the most effective way, and was hoping folks might pass on how they set up their workflows.
I am testing four fastq files currently. I have run each fiule through tophat seperately, and only combine the files at the cuffdiff stage. It still seems like there should be a more effective way (aside from batching each sample) to analyze an entire flow cell for example.
I cannot get Tophat to align all four samples, trying mutiple variations to reads1_1.
So, we can go with seprate bam files to cuffdiff, and do seem to remember something about running cuffdiff on each sample seperately.
But, at what point do you then bring more than two samples together?
Any opinions, samples workflows that you use, or hints would be greatly appreciated!
thanks,
holly
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