screen.seqs()

Commands in mothur
1

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!!!
2

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

3

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!!!
4

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

5

Hi,
I have downloaded from this website and I think it is aligned.


Thanks!!!
6

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

7

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!!!
8

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

9

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

10

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

Pat

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