Iâ€™m having a problem with .shared file formatting. I would like to kick the most abundant OTUs out of my file and re-run my analyses without them. I donâ€™t want to use split.abund for this, because that requires me to back up to before the classify steps, and would (presumably) result in some OTUs being split up.
So Iâ€™m trying to sort the .shared file by OTU size in Excel, and just break it up into three separate .shared files. But my partial files seem to have a format problem. When I run summary.single on them, there is no error message, so they are presumably being read as a proper .shared. But the .summary file has a single line with no group names, and I also get a single .rabund file with the name of the first group.
My best guess is that mothur is not detecting the line breaks in my partial .shared files. Iâ€™ve tried ending the lines with and without a tab, and it doesnâ€™t seem to help.