A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

Nelly Mostajo Berrospi; Marie Lataretu; Sebastian Krautwurst; Florian Mock; Daniel Desirò; Kevin Lamkiewicz; Maximilian Collatz; Andreas Schoen; Friedemann Weber; Manja Marz; Martin Hölzer

As we observed a lot of different sequences from LNCipedia aligning to the same positions in the genomes, we decided to condense exons at the same sequence positions, considering transcripts with one or multiple exons separately. For each contig and strand, starting from the 5' end, exons with a minimum overlap of 10 nt were grouped together. In the case of multiple exons, groups of exons were merged, if they shared any transcript origin. If all exons in the group originated from the same LNCipedia gene, the group was considered as one gene with several transcripts and its associated exon(s). Otherwise, we defined a lncRNA hot spot on gene level with several transcripts and their associated exon(s). The LNCipedia names of the gathered transcripts of a lncRNA hot spot, as well as start and end positions of all exons, are listed in the author/funder. All rights reserved. No reuse allowed without permission.