Qs: FALCON-unzip pipeline result

[olechnwin]

I'm still confused about what to do after running the pipeline. I've ran FALCON-unzip pipeline which including quiver to call high quality consensus. I got the cns_output/cns_p_ctg.fastq and cns_h_ctg.fastq. My questions:

1. if a haplotigs is within a primary contig, that means sequences in the haplotigs represent one haplotype and the primary contig represent the other haplotype?
2. What would be the best way to proceed? I was hoping to get two sets of fasta files for each of the haplotype that I can used to map RNA-seq data to identify allele-specific expression.

Thank you!