mothur

screen.seqs()

Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 439 590 151 0 3 194
25%-tile: 480 631 151 0 4 1933
Median: 498 648 151 0 4 3865
75%-tile: 513 663 151 0 5 5797
97.5%-tile: 545 695 151 0 6 7535
Maximum: 1525 1544 151 0 9 7728
Mean: 496.799 646.477 150.519 0 4.41007

of Seqs: 7728

This is my output from summary.seqs() command, can anyone help me out in getting the start and the end for the screen.seqs() command.


Thanks!!!

What are these aligned to and in which direction was the sequencing done?

Thanks for the reply Dr. Schloss,
These are aligned to RDP database.
I have one more question not concerning this but how can I assign OTUs at sequence simliarity level 0f 99% and 97% uisng furtherest neighbour method using mothur. Which command and at what parameter should I use. Please can you help me in this, is sequence similarity is same as the distance level.


Thanks!!!

why not follow the sop? is the rdp database aligned?

Hi,
I have downloaded from this website and I think it is aligned.
http://www.mothur.org/wiki/RDP_reference_files


Thanks!!!

Then these reference sequences and thus your sequences are not aligned. The output will be garbage. Please use silva.bacteria.fasta and follow the SOP.

Pat

Hi Dr. Schloss,
I have used silva also but in that there are different taxonomy for archaea, bacteria and eukaryotes , I want to do everything together not separately.
Also, I was wondering if there is way to know which of my sequences formed particular OTU, I mean to say which of my particular sequence in assigned to particular OTU in taxonomy differentiation.


Thanks for all the help!!!

then you can pool silva.bacteria.fasta, silva.eukarya.fasta, and silva.archaea.fasta and use that as your reference.

Hi ~ Pat.
How can I get the “eukarya” database??

If you go to Silva reference files you’ll find the silva reference files which include 18S sequences.

Pat

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