Hi,
I have RNA-Seq reads of mutant plant which has few insertions (unknown sequence) in comparison to wild reference genome. I want to filter out all reads which are the same as in reference so I can get only those insertion sequences. Should I map my reads straight to reference to filter it out or try to do de novo assembly and then map contigs to reference genome? What do you suggest?
I have RNA-Seq reads of mutant plant which has few insertions (unknown sequence) in comparison to wild reference genome. I want to filter out all reads which are the same as in reference so I can get only those insertion sequences. Should I map my reads straight to reference to filter it out or try to do de novo assembly and then map contigs to reference genome? What do you suggest?
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