These are chat archives for dereneaton/ipyrad

Sep 2017
Ollie White
Sep 29 2017 11:34
Hi @dereneaton @isaacovercast, is there a method of obtaining consensus sequences for all loci? I'd like to blast these against a chloroplast and mitochondrial genome and remove those loci that match from the downstream assembly if possible. Cheers
Isaac Overcast
Sep 29 2017 11:54
@Ollie_W_White_twitter There's no baked in way to do what you want. Just use one randomly selected read per locus, it'll work fine.
Isaac Overcast
Sep 29 2017 19:28
@Ollie_W_White_twitter Deren reminded me of a nice trick you can use to filter out chloroplast/mitochondrial reads. If you concatenate the chloroplast and mitochondrial reference genomes together you can use the denovo-reference assembly method to filter out all reads that map to these.