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  • Need tool to report mapped amino acid frequency per position along reference

    I need to generate translated alignments of reads along a reference (which is an amplicon that is 100% coding), and I want to report the frequency of each amino acid at each position along the reference.

    Is there some tool that can do this? My queries are illumina short reads (100mers) and I'm mapping against a ~3kb amplicon. I've done something similar in the past, but in that case I was mapping PacBio long reads that spanned the entire amplicon. In that case I could just take the exact positions of the PacBio reads that mapped from start to end of the amplicon and translate in frame 1. But this time I have short reads and it seems like it complicates things.

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