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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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reference method not adding indels #407

Open isaacovercast opened 4 years ago

isaacovercast commented 4 years ago

In the nexus output of reference assemblies you'll get stuff like this:

AGAAAAAGGCAAAACCATNNNNNNNNNNNNNNTGGCTGAAGAAAGATGGCGGAAAGATGAGAGAAGGGCAGGCAAGCAGGCTGAAGGTGAATGGTNNAAG
NNAAAAAGGCAAAACCATNNNNNNNNNNNNNNTGGCTGAAGAAAGATGGCGGAAAGATGAGAGAAGGGCAGGCAAGCAGGCTGAAGGTGAATGGTNNAAG

These should really be indels and not missing data.

isaacovercast commented 4 years ago

The indels are correct in step 3 clustS files, but they are transformed into Ns I think during step 6 (they're wrong in the clust_database file).