We will be offering mothur and R workshops throughout 2019. Learn more.

Difference between revisions of "Chimera.slayer"

From mothur
Jump to: navigation, search
Line 27: Line 27:
 
  mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer)
 
  mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer)
  
with kmer search you can adjust the ===ksize===, default ksize is 7.
+
with kmer search you can adjust the ksize, default ksize is 7.
  
 
  mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer, ksize=8)
 
  mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer, ksize=8)
  
 +
===window===
 +
The window parameter allows you to specify the window size for searching for chimeras, default=50.
  
 +
mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=400)
  
The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.
+
===increment===
 
+
The processors parameter allows you to specify how many processors you would like to use.  The default is 1.
+
The window parameter allows you to specify the window size for searching for chimeras, default=50.
+
 
The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.
 
The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.
The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.
+
 
The ksize parameter allows you to input kmersize, default is 7, used if search is kmer.  
+
mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, increment=25)
The match parameter allows you to reward matched bases in blast search, default is 5.  
+
 
The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3.  
+
 
The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4.  
+
===match & mismatch & numwanted & parents===
 +
The match parameter allows you to reward matched bases while selecting potential parents, default is 5. The mismatch parameter allows you to penalize mismatched bases while selecting potential parents, default is -4. The numwanted parameter allows you to specify how many potential parents you would each query sequence compared with, default=15. The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3.  
 +
 
 +
===minsim & mincov===
 +
The minsim parameter allows you to specify a minimum similarity between the query and the parent fragments, default=90, meaning 90%. The mincov parameter allows you to specify minimum coverage of closest matches found in template and the query. Default is 70, meaning 70%.
 +
 
 +
 
 +
===iters & minbs & minsnp===
 +
The iters parameter allows you to specify the number of bootstrap iters to do, default=100.  The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support, default=10, meaning 10%.
 +
 
 +
===divergence===
 
The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007.  
 
The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007.  
The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.
 
The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90.
 
The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%.
 
The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%.
 
The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10)
 
  
+
===processors===
chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta)
+
The processors parameter allows you to specify how many processors you would like to use.  The default is 1. If you are using the mpi-enabled version processors is set to the number of processes running.
  
chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=blast)
 
chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=400)
 
chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, numwanted=10, processors=2)
 
  
 
This command was modeled after the chimeraSlayer written by the Broad Institute.
 
This command was modeled after the chimeraSlayer written by the Broad Institute.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 16:19, 20 April 2010

The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.

Default Settings

The fasta and template parameters are required

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta)

The output to the screen looks like:

Reading sequences from core_set_aligned.imputed.fasta...Done.
Reading sequences from ex.align...Done.
Only reporting sequence supported by 90% of bootstrapped results.
gi|11093941|MNA3|AF293013	yes
gi|11093933|MNA5|AF293005	yes
gi|11093927|MND8|AF292999	yes
gi|11093924|MNF4|AF292996	yes
Processing sequence: 18

Options

search

The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer)

with kmer search you can adjust the ksize, default ksize is 7.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, search=kmer, ksize=8)

window

The window parameter allows you to specify the window size for searching for chimeras, default=50.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=400)

increment

The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.

mothur > chimera.slayer(fasta=ex.align, template=core_set_aligned.imputed.fasta, increment=25)


match & mismatch & numwanted & parents

The match parameter allows you to reward matched bases while selecting potential parents, default is 5. The mismatch parameter allows you to penalize mismatched bases while selecting potential parents, default is -4. The numwanted parameter allows you to specify how many potential parents you would each query sequence compared with, default=15. The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3.

minsim & mincov

The minsim parameter allows you to specify a minimum similarity between the query and the parent fragments, default=90, meaning 90%. The mincov parameter allows you to specify minimum coverage of closest matches found in template and the query. Default is 70, meaning 70%.


iters & minbs & minsnp

The iters parameter allows you to specify the number of bootstrap iters to do, default=100. The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support, default=10, meaning 10%.

divergence

The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007.

processors

The processors parameter allows you to specify how many processors you would like to use. The default is 1. If you are using the mpi-enabled version processors is set to the number of processes running.


This command was modeled after the chimeraSlayer written by the Broad Institute.