search

matsengrp / cft

Clonal family tree
5 stars 3 forks source link

Disallow stop codons for our CFT trees #193

Closed lauradoepker closed 7 years ago

lauradoepker commented 7 years ago

Based on my preliminary conclusions in @dunleavy005 and my ecgtheow project, I'd like to filter out all sequences with stop codons, instead of allowing them. This may clean up and clarify the conclusions we can make from our trees (hopefully).

I forget who does this filtering step (I think @psathyrella builds the stop codon info into the csv and then @metasoarous or @WSDeWitt uses it to prepare the clusters for FastTree and pruning steps)?

psathyrella commented 7 years ago

Yeah I keep every sequence that halfway-decently aligns to a BCR, and put functionality info into the annotation csv.