Difference between isoforms and paralogs in transcriptoms? I've assembled RNAseq data into a transcriptoms using Trinity. There's a option to keep only the longest isoforms for each transcripts and it lead me to wonder how it deals with duplicated genes (--&gt;transcripts). I haven't found an anwser in the original paper. Althought I reckon paralogs and isoforms are two distinct features I don't see a way to make a distinction when you only have trasncripts.
If a reference genome assembly exists, then reference-guided assembly with Trinity will keep paralogs, because it treats each genomic region as a different assembly set.
If a reference genome doesn't exist, paralogs will probably result in the construction of non-representative &quot;isoforms&quot; containing variants present in multiple genes. Inchworm does a greedy assembly of reads, so if a chimeric transcript can be constructed from the reads (which is likely with paralogous genes), then it might end up being fed to the subsequent steps. Whether that is actually emitted at the end by Butterfly will mostly depend on how the paths through the putative assemblies are traversed, which probably depends on the tolerance of Bowtie to errors.
If paralogous transcripts are sufficiently similar that the differences are within the error tolerance for assembly, then I would expect that they'd be collapsed into a single transcript.