Hi all, I'm trying to figure out a good pipeline for a de novo RNA sequencing project (hybrid assembly) - I figure I will have to use MIRA. I will have paired ~100 bp Illumina HiSeq data and am hoping to someday also get 454 FLX data (they are having trouble with the new chemistry, so I don't know when this will be). I'll be making a hybrid transcriptome assembly, then mapping the Illumina sequences to the assembly to quantify reads. This is the first time I've ever done anything like this- can people suggest pipelines that would be good to try? Also, what metrics should I be using to determine if my assembly result is good or not? I don't have a reference genome to map to.
I'm not used to command line interfaces and if anyone has used MIRA and has an example of commands they used that they can share with me, I'd be grateful.
Also, I've encountered Galaxy, which apparently can let you use MIRA with it. Has anyone done this, and had problems? Anyone have problems in general with Galaxy not allowing programs to work correctly?
Thanks for any help you can provide to this noob.
I'm not used to command line interfaces and if anyone has used MIRA and has an example of commands they used that they can share with me, I'd be grateful.
Also, I've encountered Galaxy, which apparently can let you use MIRA with it. Has anyone done this, and had problems? Anyone have problems in general with Galaxy not allowing programs to work correctly?
Thanks for any help you can provide to this noob.
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