For alignment in Oligotyping

[Tulsi Joishy]

Hello everyone,

I am trying to perform oligotyping which i could but few important parameters are still not clear to me.

1. To decide M -  How do i know that out of average reads (from all 12 samples that i have ) how many reads are for particular bacteria like Lactobacillus, Bifidobacteria etc. As the formula says that M= Avg reads per sample/1000.  For now, i took Avg counts from otu_table_summary (higlighted) (output file generated after OTU picking). 

Counts/sample summary:

 Min: 122,614.000

 Max: 173,559.000

 Median: 148,799.500

 Mean: 149,176.000

 Std. dev.: 14,219.414

 Sample Metadata Categories: None provided

 Observation Metadata Categories: taxonomy

  Is it correct. please suggest.

2. My data are Illumina generated so i didnot perform alignment. But m getting lots of entropys (which are >1.0). so m confused about my c parameters. because all entropys are not getting converged. 

Please suggest what i should correct. 

Thanking you

Tulsi

[Tulsi Joishy]

Hello everyone,

Can anyone tell me what exactly this error means

(qiime1) [qiime1@localhost Lactobacillus]$ muscle -in Lactobacillus.fasta -out Lactobacillus_aligned_muscle.fasta -diags -maxiters 4
MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

Lactobacillus 196570 seqs, max length 477, avg  length 464
Segmentation fault (core dumped)

Regards
Tulsi