Perl scripts for analysis of unmapped short reads from Hi-GRIL sequencing with the aim to find chimeras, consisting of part sRNA part mRNA.

generate_start_and_end_from_shortreads.pl

here we are preparing input files by splitting reads that could not be mapped against the reference genome into a start and an end library:

chimera_start_end_mapped_distances.pl

here we are going through the mapping results of start and end sequences and extract pairs together with distances, sequences and qualities; an optional GFF file can be specified to only store results that overlap with annotated features

chimera_annotation.pl

here we focus on a subset of annotated features (sRNAs) and create output files for each of them; the output contains all reads where either the start or end maps to the according sRNA and the feature that is either overlapped by the other start/end or lies nearby its mapping position