Blat of transcriptome to genome gave 70% hits! reality?

[pmiguel]

What is the N50 of your 15X assembly?
I would suggest using BWA or Bowtie2 to map your reads against your transcriptome. See what percent map.
Of course, depending on how "allo" your three sub-genomes are, there could be complexities there.
--
Phillip

[Brian Bushnell]

I would shred the transcriptome into pieces (~300bp or so) and map them to the genome, then calculate coverage.

[horvathdp]

I work on an auto-allo hexaploid plant species with a genome size estimated to be about 2.1 Gb. We have an excellent transcriptome assembly from four different experiments that produced about 600,000 contigs with an N50 of over 1600 bases and a CEGMA run showed 98% representation at full length and 100% representation at partial. We also have PE100 genomic sequence data from 4 different libraries from 300-400 bases in size that gives us about 15X coverage (based on kmer representation analysis). For kicks, I used BLAT to see how many genomic fragments would map to my assembled transcriptome, and got (what to me seems) a surprising number of hits. Well over 70% of the genomic fragments had hits to the transcriptome. Is this likely real, or is there something about the BLAT program that would produce a high number of spurious hits? I counted only the unique hits, so this isn't due to genomic fragments having multiple hits to the transcriptome. Thoughts? Is there a better way to determine the percentage of the genome represented in my transcriptome?