Some phased fasta with names starting with _R_?

faircloth-lab / phyluce

software for UCE (and general) phylogenomics

http://phyluce.readthedocs.org/

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Some phased fasta with names starting with _R_? #213

Closed ymilesz closed 3 years ago

ymilesz commented 3 years ago

Hi Brant,

While trying to extract SNPs from my phased UCEs, I noticed that some of the phased fasta have R in front of the usual uce-### (ex. _R_uce-12167_YMZ007_Sycophila_occidentalis_1 |_phased), and it isn't restricted to particular genes or samples. Just wondering why and if I need to be concerned about using these particular sequences downstream.

Thanks,

Miles

brantfaircloth commented 3 years ago

These have simply been reversed my MAFFT, so not an issue.

ymilesz commented 3 years ago

Perfect thank you for the quick reply!