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So I invite you to inquire when you are scheming, dreaming, pondering, planning, creating goals and visions: "What is my true Sankapla?, How can I connect with my Highest Self?" I wish you all Alignment with your Inner Divinity, your Big Love, and your Truth.
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We used the MosaikAligner in the "all" alignment mode with a hash size of 13 and 20 bp as alignment candidate threshold, allowing a maximum of 4 mismatches.
To determine which variables to consider, we align the reads to the isoform sequences and keep all alignments with at most x mismatches.
All alignments with RNAz classification score P > 0.5 were considered.
Looking at all alignments with >36% identity, 16 411 alignment boundaries changed accuracy bins.
All alignments with classification score p > 0.5 were stored as conserved secondary RNA structures.
Since highly repetitive/low complexity genomic regions may result in ambiguous or low confidence alignments, we conservatively filtered out all alignments with mapping quality (MAPQ) < 35.
Finally, we applied an alignment quality filter to the reads in U, discarding all alignments with a BLAST identity score lower than 95% and hs less than 80%.
We further removed all alignments with more than five mismatches in the first 40 colors and a mapping quality below 20.
Shown are values for all alignments with a significant MKT value (FDR-corrected p-value ≤ 0.05) and a significant BLASTx hit (1e-10) againsthehe SwissProt database.
As an additional quality control step, all alignments with a pair-wise p-distance > 0.1 between the two Chironomus species were excluded.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com