We are most generally aligning reads that are larger than the peptide-encoding reference sequences. This brings up interest in using local alignment, as seen here.
Currently, we use end-to-end alignment bu trim the low quality (right side, 3 prime) end. This could, potentially, be missing many alignments of interest.
We are most generally aligning reads that are larger than the peptide-encoding reference sequences. This brings up interest in using local alignment, as seen here.
Currently, we use end-to-end alignment bu trim the low quality (right side, 3 prime) end. This could, potentially, be missing many alignments of interest.