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Old 02-09-2011, 09:41 PM   #1
rururara
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Location: montreal

Join Date: Jan 2011
Posts: 31
Default align RNA seq to coding region

Hi everyone,

I need some opinion from people here who are mining SNP from RNA seq.
My RNA seq is from rice sample. Hence, I use rice genome from indica species as a reference genome. We know that RNA seq has a large genome. It produces large alignment file even I can't view the alignment from IGV or Artemis. I plan to try this approach:

1. align the RNA seq reads against rice coding region.
2. should i remove the NNNNNNN contain in rice genome? so that the reference genome file is not so big. furthermore the alignment is more reliable?

i hope anyone from here can share your experience and challenging in mining SNPs from RNA seq.

thanks!
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