SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cluster and cutoffs using Mothur joanaseneca Bioinformatics 0 08-29-2014 06:03 AM
ClustalO -> Why is distance matrix not quadratic? textux Bioinformatics 1 03-13-2014 04:46 AM
ncbi blast evalues > distance matrix rhinoceros Bioinformatics 0 07-24-2013 02:28 AM
Wierd overlapping paired ends with bimodal paired end distance distance distribution Mouth_Breather Illumina/Solexa 12 08-24-2012 11:06 AM
mothur then assembly? dgg32 Bioinformatics 4 11-02-2011 10:30 PM

Reply
 
Thread Tools
Old 06-28-2015, 10:36 AM   #1
dsher
Member
 
Location: Haifa, Israe;

Join Date: Feb 2013
Posts: 23
Default Very large distance matrix using MOTHUR

Hello,

We are trying to process a large dataset (~200 samples, each with ~100,000 Illumina 250bp 16S reads) using MOTHUR. We now have reached the stage of making a distance matrix to identify OTUs but this distance matrix is very large (~1.7Tb even after using the cluster.split approach). Our computational power is probably enough to run this analysis on the current dataset but we are expecting more samples, and worry that at some stage the OTU table will simply be too large.

1) Is this normal (the size)?
2) Has anyone got any experience with this sort of problem? Is there a way to divide the OTU table into sub-analyses (apart from using cluster.split) and then put them together again?

Thanks
Ashraf and Daniel
dsher is offline   Reply With Quote
Old 06-29-2015, 03:57 AM   #2
pschloss
Junior Member
 
Location: Ann Arbor, MI

Join Date: Jun 2015
Posts: 1
Default

If I had to guess, you are trying to sequence something longer than 250 nt long or you are using the 300PE V3 chemistry. If this is the case, then I'd suggest checking this out:

http://blog.mothur.org/2014/09/11/Wh...nce-matrix%3F/

Also, since we don't commonly screen the SeqAnswers forum for questions like these, it would probably be best to address questions over at www.mothur.org/forum.

Thanks,
Pat
pschloss is offline   Reply With Quote
Old 06-30-2015, 12:02 PM   #3
dsher
Member
 
Location: Haifa, Israe;

Join Date: Feb 2013
Posts: 23
Default

Thanks Pat for the reply - I have a couple of questions but will post them on the blog you mentioned rather than here. In any case if anyone else is reading this I highly recommend having a look at that blog.

Cheers
Daniel
dsher is offline   Reply With Quote
Reply

Tags
16s, distance matrix, illumina, mothur, otu

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO