I'm venturing into RNA-editing with mouse, and one of the most common methods to avoid false positives includes mapping to a transcriptome or a custom set of junction sequences followed by mapping to a genome. That's the easy part.
Once I have the mapped reads for the transcriptome, does anyone know of a good tool/method to convert those coordinates to genome coordinates while updating CIGAR strings to show split reads?
Once I have the mapped reads for the transcriptome, does anyone know of a good tool/method to convert those coordinates to genome coordinates while updating CIGAR strings to show split reads?
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