Replicates

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Replicates – Hi, I am trying to analyze some RNA-seq data using the Galaxy. The reads for each sample comes from 3 lanes, so I need to integrate these three...
Hello Medhi, Sorry for the slow reply. It's not clear from your question, but let's assume that you have 3 lanes of RNA-seq data for each of...
RNA seq analysis – Hi Jeremy, I thought I'd write to get a discussion of a workflow for people doing RNA seq that I have found very useful and addresses some issu...
Hi David, This is a really interesting workflow. My comments: (1) I encourage you to start a discussion about this idea on seqanswers.com; y...
HI Jeremy, Thanks for the feedback. I know what you mean about tophat not having the same functionality of bowtie. However, I think whatever to...
Hello, I like your approach of running the alignment tools with liberal settings and then filtering the results into different categories. ...
Thanks Ann for your comments and for the stuff you showed at IGB - looks very interesting. I agree that multihits may the equivalent of the proble...
Hello, I like your approach of running the alignment tools with liberal settings and then filtering the results into different categories. ...
David,   Just curious are you using  latest version of TopHat ( 1.2.0 released on 01/18/11). I was in contact with TopHat team about similar iss...
Hi all, Further to my last email, I've published a workflow (Bristol workflow ....) which does what I described below - hope this helps in unde...