ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data.

ABSTRACT:

Background

With the advances in next-generation sequencing technologies, it is possible to determine RNA-RNA interaction and RNA structure predictions on a genome-wide level. The reads from these experiments usually are chimeric, with each arm generated from one of the interaction partners. Owing to short read lengths, often these sequenced arms ambiguously map to multiple locations. Thus, inferring the origin of these can be quite complicated. Here we present ChiRA, a generic framework for sensitive annotation of these chimeric reads, which in turn can be used to predict the sequenced hybrids.

Results

Grouping reference loci on the basis of aligned common reads and quantification improved the handling of the multi-mapped reads in contrast to common strategies such as the se

SUBMITTER: Videm P 

PROVIDER: S-EPMC7844879 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature