NanoPARE

NanoPARE is a set of tools for the analysis of 5' RNA data from nanoPARE sequencing libraries. The NanoPARE package contains (1) EndMap for Aligning 5P and BODY FASTQ files to a reference genome, (2) EndGraph for Identifying 5P features, (3) EndClass for Classifying 5P features as capped or noncapped and label features according to a reference transcriptome, (3) EndMask for Masking genomic regions with capped features and converting genome coordinates to transcriptome coordinates, (4) EndCut for searching evidence of small RNA mediated cleavage in transcript-mapping noncapped 5P reads. Requirements: STAR aligner 2.5+, Python 3.6+, Samtools 1.3+, Bedtools 2.26, and Cutadapt 1.9.