Comprehensive Transcript Alignment Analysis

Reconstructed transcripts were mapped to genome sequences using GMAP, reporting only the single top scoring alignment per sequence. Individual introns and complete splicing patterns were extracted from each of the alignments and compared to reference annotations using custom PERL scripts. Unique introns (missing from the reference annotations) were required to contain consensus dinucleotide splice sites (GT or GC donors and AG acceptors).

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Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N, & Regev A. (2011). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology, 29(7), 644-652.

Publication 2011

Dinucleotide Donors Introns Sequence alignment

Corresponding Organization :

Other organizations : Broad Institute, Massachusetts Institute of Technology, University of Massachusetts Chan Medical School, Science for Life Laboratory, Uppsala University, Hebrew University of Jerusalem

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Protocol cited in 473 other protocols

Variable analysis

independent variables

Genome sequences

dependent variables

Reconstructed transcripts
Introns
Splicing patterns

control variables

Reference annotations

controls

Positive control: Consensus dinucleotide splice sites (GT or GC donors and AG acceptors) for unique introns
Negative control: Not explicitly mentioned

Annotations

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