How to manual-free recognize which known transcript/isoform the alignment/mapping is, given the existence of sequencing error and alignment/mapping error? Further, judge a alignment/mapping is a novel transcript/isoform?
It seems many transcript assembly or detection softwares, like Cufflinks could provide transcript sequence (in FASTA) or exon junction (in GTF), with either no accession or their own accessions. Does anyone known any tool can handle this, or any convenient method?
Thanks in advance!