URL: http://woldlab.caltech.edu/rnaseq
Proper Citation: ERANGE (RRID:SCR_005240)
Description: Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.
Abbreviations: ERANGE
Synonyms: Enhanced Read Analysis of Gene Expression
Resource Type: software resource
Defining Citation: PMID:18516045
Keywords: transcriptome, rna-seq, bio.tools
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