PARANOiD is a versatile software for fully automated analysis of iCLIP and iCLIP2 data. It contains all steps necessary for preprocessing, the determination of cross-link locations and several additional steps, which can be used to detect specific characteristics, e.g. definite distances between cross-link events or identify binding motifs. The cross-link sites are presented as WIG files that can be easily visualized e.g. using IGV, for which a config file is offered. Additionally, results are offered as statistical plots for a quick overview and as standardized bioinformatics file formats or TSV files, which can be used for further analysis steps. The data provided are used as a test case for PARANOiD. The data was extracted from RVFV MP-12 virions (virion-reads-M-fragment-only.fastq) and BHK cells infected with RVFV (BHK-reads-M-fragment-only.fastq) applying the iCLIP2 method for RVFV N iCLIP. Three independent biological replicates were performed for each sample. Sequencing was performed using the MiSeq Sequencer (Illumina) with MiSeq Reagent Kit v2 Micro (Illumina) for N-iCLIP from virus particles and MiSeq Reagent Kit v3 (Illumina) for N-iCLIP from infected BHK cells. The original reads have been aligned to the RVFV MP-12 reference genome and only reads aligning to the M-fragments were extracted. The whole dataset will be publish at a later date File description: virion-reads-M-fragment-only.fastq - Reads obtained from RVFV virions BHK-reads-M-fragment-only.fastq - Reads obtained from BHK cells infected with RVFV reference_RVFV.fasta - RVFV MP-12 reference genome barcodes-RVFV.tsv - Barcodes for virion-reads-M-fragment-only.fastq barcodes-RVFV-merge-all.tsv - Barcodes for merging all samples of virion-reads-M-fragment-only.fastq barcodes-BHK.tsv - Barcodes for BHK-reads-M-fragment-only.fastq barcodes-BHK-merge-all.tsv - Barcodes for merging all relevant samples of BHK-reads-M-fragment-only.fastq

The project was funded by following sources: Deutsche Forschungsgemeinschaft (DFG) Research Training Group (RTG) 2355 (project number 325443116) Deutsche Forschungsgemeinschaft (DFG) SFB1021 project ID 197785619, Z02 MCIN/AEI /10.13039/501100011033 / FEDER, UE grant PID2021122567-OB100