Benchmark data used in the evaluation of ChiRA tool-suite.

The reads generated mimic CLASH experimental data. Each read is a fusion of a human hg38 miRBase mature miRNAs and some random TargetScan target sequences. The numbers 10, 12, 15, 18, and 20 in the file names represent the length of the chimeric arms. The are 1million reads in FASTA file. Files with "Insert" in their names contain a short 5 nt random sequence, whereas the "noInsert" files do not.  TargetScanSites_merged.fa.fasta and hg38_MIR_mature.fa.fasta contain the reference sequences. The sequence identifiers in the FASTA file are in the following format:

>hsa-miR-193b-5p_MIMAT0004767:1-20||chr7:114656010-114656173+:82-95

where,

• hsa-miR-193b-5p_MIMAT0004767 is the sequence ID of the miRNA from which first chimeric arm of this read was derived from. This ID can be found in hg38_MIR_mature.fa.fasta.
• 1-20 represents the 1-based start and end positions on hsa-miR-193b-5p_MIMAT0004767 representing the origin of the first chimeric arm.
• chr7:114656010-114656173+ is the sequence ID of the TargetScan target site from which the second chimeric arm of this read was derived from. This ID can be found in TargetScanSites_merged.fa.fasta
• 82-95 represents the 1-based start and end positions on chr7:114656010-114656173+ representing the origin of the second chimeric arm.