[adegenet-forum] different number of individuals in fastas

[Katharine Coykendall]

Figured it out!  In one of my fasta files, I had three of the sample names
capitalized and the other file they weren't.

On Thu, Feb 22, 2018 at 3:34 PM, Katharine Coykendall <dollykc at gmail.com>
wrote:

> Hello,
>  I've been following the instructions found at  http://popgen.nescent.org/
> PopDiffSequenceData.html to do a hierarchical F analysis on my data.  I
> have two fasta files with the same 117 individuals in each file.  The files
> are different genes.  When I put them together using the read.multiFASTA
> command, it tells me that there are 120 sequences.  When I turn it into a
> genid object it says there are 120 individuals and 19 alleles.  I checked
> both files to make sure that the sample names are the same between them and
> they are. I was wondering if it had to do with add.gaps=TRUE so I tried to
> set it to false, but I get an error
> Error in file(con, "rb") : cannot open the connection
> In addition: Warning message:
> In file(con, "rb") : cannot open file 'FALSE': No such file or directory
>
> Is there an easy way to look at the multiFASTA or genid file to see where
> the extra three individuals are coming from?
>
> Thanks,
> Katharine
>
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