Great day all,
I'm a novice to the use of mothur and currently following the guide MiSeq_SOP. However, I faced several problems here but couldn't be solved and I would like to have your guidance.The problems are listed below:
1.Processing Improved Sequences Section I followed the guide and all were the same output until the command pre.cluster. which generated different output from the one shown in the Miseq_SOP. The file attached below is the log of my commands. The unique sequence I got was 3909 which differ from the website which stated 5721. May I know did I key in wrongly? However, though I got a different result, I proceeded to the summary.seqs. and the table showed different values.
2.Assessing Error section. The first task of the get.group command indicates that the 'Mock' group were not available and I got a very different output once again. Despite that, I still proceed and reached to analysis section
3.Analysis section For the dist.shared command for beta diversity measurement, I failed to proceed due to the statement - not enough valid group. This might be due to the number I keyed which is 2392 as written on the website.
Could all these problem be due to the stability.files from the beginning section? Because on the website it stated 22 files for 3 females and a mock group. But, I only found 21 files for the 3 females and a mock group. I'm using the latest version mothur (mothur v.1.39.5) for windows 10.