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!
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!