make.biom doesn't exist

Commands in mothur
1

Hi

I want to covert my taxonomy and OTU file to biom format but when I’m trying it shows an error saying the “Invalid command”.
I don’t whats wrong with it!!
If some one has faced the same error please help me out.


Cheers, Rich
2

What version of mothur are you using?

3

I’m using mothur v.1.22.2 on 32 bit Ubuntu machine.

4

Thank you!!
I have upgraded it to newer version and now the command is working.

5

all i did was ask a question :slight_smile:

6

Hello,
After taxonomy assignment I get lots of unclassified sequences and I there abundance is not low.
I don’t want to lose unclassified sequences. Is there anyway to assign taxonomy to such sequences?


Thanks in advance
7

Unclassified at what level? Why would you lose them? It is generally difficult to classify short sequences to the genus level, so you may be stuck with what you’ve got.

8

Thanks for reply
Yes you are right maximum unclassified sequences are at genus and species level. But if i want to make bar graph at genus level how can i avoid to exclude these sequences/OTUs
Otu3224 18 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;unclassified;unclassified;


but there are few which has not been classified after kingdom level Otu3037 1 k__Bacteria;unclassified;unclassified;unclassified;unclassified;unclassified;unclassified; whats the solution for these ones.

Thanks in advance

9

Yes you are right maximum unclassified sequences are at genus and species level. But if i want to make bar graph at genus level how can i avoid to exclude these sequences/OTUs
Otu3224 18 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;unclassified;unclassified;

I would argue that is their genus - unclassified Ruminococcaceae.

Otu3037 1 k__Bacteria;unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;

Again, that is a “genus”. For either situation you could use something like the following in remove.lineage:

taxon=f__Ruminococcaceae;unclassified

or

taxon=k__Bacteria;unclassified;

10

Just to make sure I have got your point correctly
You mean to say I should use the neighboring name as pseudo name
Otu3224 18 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__unclassified(Ruminococcaceae);s__unclassified(Ruminococcaceae);

and for other(below) I should remove the lineage because it has not been classified at alla after Kingdom.
Otu3037 1 k__Bacteria;unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;


And another thing is if want to include sample names also. Can we use tax.summary file? What does RankID means? Is the same solution is applicable there for unclassified?

Thanks for your reply
Cheers,

11

I’m not clear what you’re asking about pseudonames… mothur would treat both of your OTUs as separate genera in the summary file and after running phylotype.