RVFV data aligning only to M-Fragment to test the PARANOiD pipeline

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