The PARA-suite – PAR-CLIP specific sequence read simulation and processing

Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein-RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into nascent transcripts leads to high rates of specific nucleotide conversions during reverse transcription. So far, the specific properties of PAR-CLIP-derived sequencing reads have not been assessed in depth.

Researchers at the Heinrich-Heine Universität Düsseldorf compared PAR-CLIP sequencing reads to regular transcriptome sequencing reads (RNA-Seq) to identify distinctive properties that are relevant for reference-based read alignment of PAR-CLIP datasets. They also developed a set of freely available tools for PAR-CLIP data analysis, called the PAR-CLIP analyzer suite (PARA-suite). The PARA-suite includes error model inference, PAR-CLIP read simulation based on PAR-CLIP specific properties, a full read alignment pipeline with a modified Burrows-Wheeler Aligner algorithm and CLIP read clustering for binding site detection.

The PARA-suite


(A) The PARA-suite. Dashed boxes represent software packages; all other boxes represent executable programs. The Utils package includes tools for working with error-prone sequencing data and the postprocessing package contains a tool for clustering an aligned PAR-CLIP dataset to identify RBP-bound genomic regions. (B) Read alignment by a fast read aligner is necessary to infer the error profile for a particular read dataset (we selected BWA). (C) BWA PARA is applied to the entire dataset to map error-prone reads, indicated here by the additional mapping of the two reads (shown in blue). (D) An optional alignment versus a transcriptome reference database can be executed using BWA PARA to identify previously unmapped reads.

The researchers show that differences in the error profiles of PAR-CLIP reads relative to regular transcriptome sequencing reads (RNA-Seq) make a distinct processing advantageous. They examine the alignment accuracy of commonly applied read aligners on 10 simulated PAR-CLIP datasets using different parameter settings and identified the most accurate setup among those read aligners. They demonstrate the performance of the PARA-suite in conjunction with different binding site detection algorithms on several real PAR-CLIP and HITS-CLIP datasets. This processing pipeline allowed the improvement of both alignment and binding site detection accuracy.

Availability – The PARA-suite toolkit and the PARA-suite aligner are available at and, respectively, under the GNU GPLv3 license.

Kloetgen A, Borkhardt A, Hoell JI, McHardy AC. (2016) The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ 4:e2619. [article]

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