Why are there shorter contigs from transcriptome assembly than from a whole genome assembly? I know the difference between transcriptome and genome, but don't really understand what contigs are in the context of sequencing in bioinformatics, and why are the contigs shorter in transcriptome assembly than in whole genome assembly. Anyone mind explaining? Much appreciated.
The longest possible transcriptome contig reflects the longest possible transcript. In the human genome, that's possibly Titin, which is ~35K aa (that's ~105Kb) and will be longer pre-splicing.
The longest possible genome contig reflects the longest chromosome. In the human genome that's chr1 at ~250Mb.
In practise your contigs/scaffolds will be a lot shorter for various reasons (e.g. hard to sequence the telomeres and repeats) but it illustrates the difference since all the chromosomes consist of contiguous DNA but many separate RNA transcripts (and not all DNA is transcribed).