Use este identificador para citar ou linkar para este item: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1126751
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dc.contributor.authorPADILHA, L.
dc.contributor.authorCAIXETA, E. T.
dc.contributor.authorSILVA, F. R. da
dc.date.accessioned2020-11-19T09:11:49Z-
dc.date.available2020-11-19T09:11:49Z-
dc.date.created2020-11-18
dc.date.issued2012
dc.identifier.citationIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTACIONAL BIOLOGY, 8., 2012, Campinas, São Paulo. Resumos... Campinas, SP, 2012.
dc.identifier.urihttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1126751-
dc.descriptionNew sequencing technologies brought deep probing of transcriptomes (so-called RNAseq) to the reach of individual researches. Analysis of RNAseq sequences, however, depend on the alignment of reads to a reference genome. Some approaches have been proposed to allow de novo assembly of the transcripts, therefore allowing RNAseq to be used on organisms lacking a reference genome. The efficiency of those approaches, however, were tested only with diploid species. Here we propose a methodology to evaluate the results of de novo assembly of allotetraploid Coffea arabica RNAseq reads obtained from libraries of coffee leaves infected by Hemileia vastatrix. Trinity was able to assemble longer transcripts when compared to ABySS, SOAPdenovo and Oases. Moreover, the transcripts assembled by Trinity where more similar to the ones obtained using Cufflinks after aligning the RNAseq to 10 Coffea sp. publically available BAC sequences. Comparison of the most abundant transcripts with several Coffea sp. single copy described genes, though, shows that all assemblers failed to perfectly reconstruct the transcripts.
dc.language.isoeng
dc.rightsopenAccesseng
dc.titleComparing methods of RNAseq analysis for species without a reference genome.
dc.typeResumo em anais e proceedings
dc.subject.thesagroCoffea Arábica
dc.subject.thesagroGenoma
dc.subject.nalthesaurusTranscriptome
dc.description.notesX-MEETING.
riaa.ainfo.id1126751
riaa.ainfo.lastupdate2020-11-18
dc.contributor.institutionLILIAN PADILHA, CNPCa; EVELINE TEIXEIRA CAIXETA MOURA, CNPCa; FELIPE RODRIGUES DA SILVA, CNPTIA.
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