I came to know that N50 value is not an important parameter to determine the Assembly quality in Transcriptome assembly rather it can be applicable in Genome assembly. Is it true?, although we know N50 value is also changeable with more mismatches so can't rely on that fully. Can any one comment on this??
N50 is not as useful in a transcriptome assembly as genome. In a genome, a low N50 (few contigs) and high L50 (long contigs) are good. But in a transcriptome, it really depends on the organism - you want the contigs to reflect the organism's genes and isoforms, rather than just being as long as possible.