Hello, I'm a newbie of bioinformatics.

I had a some curious about in mapping process.

In general mapping process, we mainly mapped reads to reference genome of species.

However, if we don't have a reference genome, we used De novo assembly, then make transcriptome.

After that we mapped reads to transcript assembly.

At this time, why does ambiguity increase??

I think one of the reason is alternative splicing.

Also, maybe In transcription process, intron was filtered out, so in transcriptome there were only exon region. so it makes increasing of ambiguity.

Can you guys explain for me?