Workflow from Scientific Research

The short-read RNA sequencing data is aligned using the provided annotation file, and reads are classified into uniquely mapped and multi-mapped reads based on the alignment score. Uniquely mapped reads and multi-mapped reads are then aligned to TE A, TE B, and TE C. Long-read RNA sequencing, preferably ONT, is aligned using minimap2 [ 18 ], and TEs are quantified using featureCounts [ 19 ] with the same annotation file provided for short-read RNA sequencing. TPM counts for long-reads are calculated, and the belonging subfamily is provided for each individual TE.

DOI