Merge the count file

When I use the command “sub.sample(…size=6000,persample=true)”, the program delete the sample which sequence number less than 6000. There are 5 sample removed, but I want to merge one sample back.

So, I used command “get.groups” to extract the particular sample before sub-sampling. I get one fasta file and one count file. I can merge the fasta file to the subsampled fasta file. But I can not merge the count file to the subsampled count file.

Is there any solution? Thank you very much

Why not use remove.groups to remove the 4 other samples?

I have 20 sample in the beginning. 15 of them more than 6000, 4 of them less than 1000, the other sequence number is around 3000.
For the sample more than 6000, i want to normalize their sequence number to 6000 by using sub-sampling. And keep the sample whose sequence number is around 3000 without any change.

I want to use these 16 sample to do my analysis. Thank you !

There’s not currently a way to do that in mothur and I have to add, I’m not sure that I would encourage anyone to do that. All of the samples need to have the same number of sequences. Remember that virtually all methods are biases by different sampling levels.