I am using OASES to do transcriptome de novo assembly. I tried multiple kmer values and were able to choose the best one based on N50, larges transcripts and so on. how ever, I am wondering if it makes sense to merge assemblies produced with different kmers.
another question would be dealing with the un-used reads, should be also merge them with multiple transcripts.fa ?
Will be happy if anyone give me a hint. Thanks in advance.