Hi!
I am working with a functional gene, so working on proteins… I have made a distance matrix in ARB …and used the cluster (Phylip=…) command to work with the OPU…Now I want to get the table that indicates the number of times an OTU shows up in each sample… so a . shared file, which I have done…but I do not know how to get which sample correspond to the OTU on the table…it is just marked as OTU001, OTU002 etc… Does it correspond to the .list file? If it does, my second problem is that when I normalize, the number of OTU change and therefore the .list file is no good no more… I do not know where I could know to which sample the OTU s correspond…and therefore what they are!
Many thanks!
kim
“I do not know how to get which sample correspond to the OTU on the table…it is just marked as OTU001, OTU002 etc… Does it correspond to the .list file?”
Yes, the OTUs in the shared file relate to the OTUs in the list file.
" If it does, my second problem is that when I normalize, the number of OTU change and therefore the .list file is no good no more… I do not know where I could know to which sample the OTU s correspond…and therefore what they are!"
You can run the sub.sample command on the list and group file and then run make.shared.
sub.sample(list=final.an.list, group=final.groups, size=yourSize)
make.shared()
I hope this help,
Sarah
Actually by doing this it does not give me the same number of sequences per sample…It gives me a shared file with my Size as the total number of sequences ( all samples together)… :?
Sorry, try this:
sub.sample(list=final.an.list, group=final.groups, size=yourSize, persample=T)
make.shared()