I am relatively new to mothur and I am following instructiions from Miseq SOP (mothur wiki) with my illumina sequencing data.
I have encountered error at the make.shared command and unable to to do OTU based analysis without the .shared file
make.shared(list=LSF.R1.clean.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list, count=LSF.R1.clean.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table, label=0.03)
[ERROR]: Your count file does not have group info, aborting.
[ERROR]: did not complete make.shared.
I read the make.shared mothur wiki page and it showed the list and count files were sufficient to create a shared file.
I am not sure if the information im giving below is relevant, however i want to give a brief overview of my method to give an idea about my problem.
My sample is soil microbiome and I have 2 samples with different conditions. So I recieved 2 sets of ffastq and rfastq files from the sequencing company. I have been analysing both the samples seperately. for ex ffastq1 and rfastq1 in folder A ; ffastq2 and rfastq2 in folder B. I run mothur seperately from inside both folders.
I do not have a mock group.
Please help me with this problem. I appreciate any help.
i apologize in advance if i seem to have misunderstood the meaning of some command.