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Analysis of chimeric reads from RNA-seq data

ABSTRACT: RNA-seq analysis of Drosophila pharate adults Total RNA extracted from four lines of Drosophila melanogaster pharate adults were depleted of ribosomal RNAs and sequenced.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Zhipeng Lu

PROVIDER: E-GEOD-50711 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.

Lu Zhipeng Z Matera A Gregory AG

Nucleic acids research 20140312 9

Non-coding (nc)RNAs are important structural and regulatory molecules. Accurate determination of the primary sequence and secondary structure of ncRNAs is important for understanding their functions. During cDNA synthesis, RNA 3' end stem-loops can self-prime reverse transcription, creating RNA-cDNA chimeras. We found that chimeric RNA-cDNA fragments can also be detected at 5' end stem-loops, although at much lower frequency. Using the Gubler-Hoffman method, both types of chimeric fragments can ...[more]

PMID: 24623808

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Analysis of chimeric reads from RNA-seq data

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