How to know if it is missing a gene or assembly error?
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2.1 years ago
DNAngel ▴ 240

Hello all,

Just wondering - after assembling my reads to a reference protein-coding sequence for a bunch of genes, I happened to notice that for a couple certain clades I just did not get any sequence from them. Is this a case of a gene being lost in the clade, or are their particular sequences too divergent to be mapped to my reference? Is there a way to tell? I wlll also mention some random other species missing the gene (no sequence obtained) but nothing as consistent as from a whole clade. This was from target exon capture.

BWA Bioinformatics Assembly • 345 views

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