We are trying to decide between MiSeq and 454 FLX for a MHC genotyping project in one bird species (MHC class II B exon2, 180bp). After running a preliminary run on Roche Junior and carefully filtering out artefacts, we found we need a very large sequencing depth to saturate the variability of alleles in each individual (up to tens of alleles). For the full experiment of multiplexing and genotyping amplicons of 200+ individuals I would prefer MiSeq over Titanium given the price/performance. But amplicon sequencing on Illumina may get tricky even with less problematic loci than MHC (low complexity problem). Plus I heard about huge headaches when analysing MHC data from Illumina (troubles with distinguishing true alleles from erroneous reads).
Does anyone have any experience with sequencing MHC amplicons on Illumina. I'd be grateful for any comments/recommendations.
Does anyone have any experience with sequencing MHC amplicons on Illumina. I'd be grateful for any comments/recommendations.