Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • cluster and cutoffs using Mothur

    Hello,

    I've been using QIIME and Mothur to analyse different sets of 454 data, and this is a little off topic, because it's related to Sanger data... still I think my problem can also happen with NGS data.

    So, I have Sanger generated data for a functional gene and I want to use Mothur to acess the existance of OTU's...(i.e create a distance matrix and cluster, according to a given cutoff).

    I produced an alignment in fasta format, created the phylip distance matrix (column formatted) using the dist.seqs command, as follows:

    dist.seqs(fasta=aligned.fas, output=squared)

    then I clustered using the cluster command, as follows:

    cluster(phylip=aligned.square.dist, cutoff=0.05)

    Hence, the list file should give me a list of the existing OTU's at different levels, but I only get those that are unique, 0.01, 0.02 and 0.05... and I'd like have information regarding the 0.03 cutoff, because I want to compare the clusters I get with a 0.02 and 0.03 cutoff (98% and 97% respectively).

    I've tried to set the cutoff to 0.04, 0.03, I've played with the "hard=t" and the "precision" options, and I still can't figure this out... can someone help me with this, please?

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:35 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
21 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-06-2024, 07:17 AM
0 responses
19 views
0 likes
Last Post seqadmin  
Working...
X