A bioinformatics workflow for the analysis of transcriptome data generated by deep-sequencing

Torna indietro

Abstract

The huge amount of transcript data produced by high-throughput sequencing requires the development and implementation of suitable bioinformatic workflows for their analysis and interpretation. These analysis workflows, including different modules, should be specifically designed also based on the sequencing platform (Roche 454, Illumina, SOLiD) and the nature of the data (polyA or total RNA fraction, strand specificity). In the case of cDNA obtained from a total RNA preparation, in addition to polyadenylated protein coding mRNAs, a great variety of transcript sequences can be obtained, including ribosomal RNAs, mitochondrial transcripts and a large variety of functional non coding RNAs (ncRNAs). To deal with these data the analysis workflow should include specific modules to distinguish ncRNAs fractions from the large number of other functional proteincoding transcripts. To this aim we developed an analysis pipeline that, given as input a large collection of reads (particularly from Roche 454), provides the expression profile at qualitative and quantitative level of human mtDNA, ribosomal RNAs, ncRNAs and protein coding mRNAs.

Autore Pugliese

Tutti gli autori

  • Licciulli F.; Caratozzolo F.M.; Cornacchia S.; D'Elia D.; D'Erchia A.M.; Fosso B.; Grillo G.; Liuni S.; Mangiulli M.; Manzari C.; Mignone F.; Paluscio A.M.; Picardi E.; Sbisà; Tullo A.; Pesole G.

Titolo volume/Rivista

Non Disponibile

Anno di pubblicazione

2010

ISSN

Non Disponibile

ISBN

978-88-6194-079-6

Numero di citazioni Wos

Nessuna citazione

Ultimo Aggiornamento Citazioni

Non Disponibile

Numero di citazioni Scopus

Non Disponibile

Ultimo Aggiornamento Citazioni

Non Disponibile

Settori ERC

Non Disponibile

Codici ASJC

Non Disponibile