I used a homemade skript to screen shared file for certain otu-s.(OTU-s that according to relabund file have abundace of at least 0.01 in at least one sample).
This is the resulting file.
When I do run venn command with my produced shared file venn(shared=MNP.screened.shared) then it’ll only run it for the first group … so output will only be one circle enne.svg. If i try to force it frex. venn(shared=MNP.screened.shared, groups=peale-mehed)then it says the other ones are not legal groups.
If I re-arrange the lines of .csv file in Libreoffice it’ll gladly take any first line to make the “venn diagramm” for but will ignore the second and third lines.
I was thinking that maybe there is a problem with the newlines, but as I see both my homeskript and mothur should produce files with Unix style newlines?
What else could there be wrong in my file format wise so that it refuses to read next two lines? Can anybody help me with that?
If not or even if yes - does anybody have any suggestions how I might accomplish that - venn diagram for OTU-s that have certain minimal relative abundance. Is it in general possible to get shared files that are screened as following by mothur own commands?
It doesn’t look like you have 5900 OTUs in that shared file. I think mothur is reading the entire file as the first group.
AHH. So blindingly obvious. Thank you! Everything works out fine when I revise the number of OTU-s field. Seems the mothur will look at this field and then tries to read in as many otus as specified there?
Thank you again now it seems that I can actually use my scripts to sort stuff out if needed.