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Split.abund

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The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups.

Default Settings

The split.abund command parameters are fasta, list, name, count, cutoff, group, label, groups and accnos. The fasta and a list or name parameter are required, and you must provide a cutoff value.

Using a list file the splitting is done based on the size of the otus.

mothur > split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, cutoff=10)

Opening abrecovery.fn.rare.list you would see:

unique	242	AY457723	AY457741	AY457686	AY457855   AY457698 ...	
0.00	230	AY457723	AY457741	AY457686	AY457855   AY457698 ...	
0.01	204	AY457723	AY457741	AY457686	AY457855   AY457698 ...				
0.02	185	AY457723	AY457741	AY457686	AY457855   AY457698 ... 		
0.03	168	AY457723	AY457741	AY457686	AY457855   AY457698 ... 
...	

Opening abrecovery.fn.abund.list you would see:

0.07	4	AY457701,AY457774,AY457838,AY457715,AY457859,AY457747,AY457809,AY457780,AY457763,AY457755,...	
0.08	4	AY457701,AY457774,AY457838,AY457715,AY457859,AY457747,AY457809,AY457780,AY457763,AY457755,...	
0.09	4	AY457864,AY457754,AY457910,AY457871,AY457701,AY457774,AY457838,AY457715,AY457859,AY457747,...
...

or

Using a names file the splitting is done based on the number of sequences a sequence represents.

mothur > split.abund(fasta=abrecovery.fasta, name=abrecovery.names, cutoff=10)

Since the names file does not contain any sequences that represent more than 10 other sequences, you only get .rare files.

or

Using a count file the splitting is done based on the number of sequences a sequence represents.

mothur > split.abund(fasta=abrecovery.fasta, count=abrecovery.count_table, cutoff=10)

Since the count file does not contain any sequences that represent more than 10 other sequences, you only get .rare files.


cutoff

The cutoff parameter is used to qualify what is abundant and rare. A grouping is determined to be abundant if it contains more sequences than the cutoff.

group

The group parameter allows you to parse a group file into rare and abundant groups.

mothur > split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, cutoff=10, group=abrecovery.groups)

groups

The groups parameter allows you to parse the files into rare and abundant files by group. For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files. If you want .abund and .rare files for all groups, set groups=all.

 mothur > split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, cutoff=10, group=abrecovery.groups, groups=all)

label

The label parameter is used to read specific labels in your listfile you want to use.

mothur > split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, cutoff=10, label=0.10)

accnos

The accnos parameter allows you to output a .rare.accnos and .abund.accnos files to use with the get.seqs and remove.seqs commands.

mothur > split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, cutoff=10, accnos=true)

Revisions

  • 1.28.0 Added count option