Hi folks, I am a newcomer to NGS data analysis. I read two papers regarding the application of TopHat and PASS respectively to carry out NGS reads mapping to reference genome. Has anyone had any experiences dealing with those two programs? Which one might be a better choice to use when trying to map Illumina reads to reference genome to identify mismatches? Any option in TopHat to implement in order to record the mismatch coordinates?
Thanks!
Thanks!
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