After running filter.seqs I’m finding that all of my columns have been removed. It doesn’t look like this forum has a search option anymore (at least there isn’t a search bar visible in my browser). I believe there’s already a thread for this but when I try to search this in google it won’t allow me access to those pages. All that comes up is the following error:
"Information
Sorry but you are not permitted to use the search system."
Any help with either issue is greatly appreciated!
I usually finds that this happens when the sequences haven’t been properly aligned/screened prior to filtering. What does the output of summary.seqs() on your aligned sequences look like?
This is after alignseqs:
2.5%-tile: 1968 11550 252 0 4 270510
25%-tile: 1968 11550 253 0 4 2705093
Median: 1968 11550 253 0 5 5410186
75%-tile: 1968 11550 253 0 6 8115278
97.5%-tile: 1968 11550 253 0 6 10549861
Maximum: 13425 13425 273 0 16 10820370
Mean: 1972.54 11540.2 252.537 0 4.88631
total # of seqs: 10820370
In screen.seqs you need to say start=1968, end=11550. You have a sequence that starts and ends at 13425, so there is a . in every column. When you do filter.seqs(trump=T), that wipes out all of the columns.