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Difference between revisions of "Get.mimarkspackage"

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(Created page with "The get.mimarkspackage command creates a MIMarks package template for your samples for the environment you select. See Creating a new submission to see how to use make.sra in ...")
 
(Revisions)
 
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==Revisions==
 
==Revisions==
 
* 1.34.0 First Introduced.
 
* 1.34.0 First Introduced.
 +
* 1.38.1 Fixes group name issue with oligos file option so that it work with make.sra command.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 19:29, 9 August 2016

The get.mimarkspackage command creates a MIMarks package template for your samples for the environment you select. See Creating a new submission to see how to use make.sra in your workflow.

Default Options

You must provide a file, oligos or group file. Mothur uses the file, oligos and group file to extract your sample names.

mothur > get.mimarkspackage(file=test.file)

or

mothur > get.mimarkspackage(oligos=GQY1XT001.oligos)

or

mothur > get.mimarkspackage(group=final.groups)

This command will create a template that looks like:

#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages.
#Please fill all the required fields indicated with '*'
#Unknown or inapplicable fields can be assigned 'missing' value.
#You may add extra custom fields to this template. Make sure all the fields are separated by tabs.
#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs.
#You can edit this template using Microsoft Excel or any other editor. But while saving the file please make sure to save them as 'TAB-DELIMITED' TEXT FILE.
#MIMARKS.survey.host-associated.4.0
#{sample name}	{description of sample}	{sample title}	{description of library_construction_protocol}	{http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock}	{Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (eg., 30-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm" or "YYYY-mm-ddThh:mm:ss" (eg., 1990-10-30, 1990-10 or 1990-10-30T14:41:36)}	{descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO}	{descriptor of the local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO}	{material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO}	{Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"}	{The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".}	{The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W}
#{text}	{text}	{text}	{text}	{controlled vacabulary}	Template:Timestamp	Template:Term	Template:Term	Template:Term	{{term}:{term}:{text}}	Template:None	{{float} {float}}
*sample_name	*description	*sample_title	*seq_methods	*organism	*collection_date	*env_biome	*env_feature	*env_material	*geo_loc_name	*host	*lat_lon
F003D000_AATGGTAC.CCGTCAATTCMTTTRAGT	
F003D002_AACCTGGC.CCGTCAATTCMTTTRAGT	
F003D004_TTCGTGGC.CCGTCAATTCMTTTRAGT	
F003D006_TTCTTGAC.CCGTCAATTCMTTTRAGT	
F003D008_TTCGCGAC.CCGTCAATTCMTTTRAGT	
F003D142_TCCAGAAC.CCGTCAATTCMTTTRAGT	
F003D144_AAGGCCTC.CCGTCAATTCMTTTRAGT	
F003D146_TGACCGTC.CCGTCAATTCMTTTRAGT	
F003D148_AGGTTGTC.CCGTCAATTCMTTTRAGT	
F003D150_TGGTGAAC.CCGTCAATTCMTTTRAGT	
MOCK.GQY1XT001_AACCGTGTC.CCGTCAATTCMTTTRAGT	

Options

file

The file parameter is used to provide a file containing a list of individual fastq or sff files or paired fastq files with a group assignment. File lines can be 2 or 3 columns. The 2 column files are sff file then oligos or fastqfile then oligos. You may have multiple lines in the file. The 3 column files are for paired read libraries. The format is groupName, forwardFastqFile reverseFastqFile. This is the same file you will later use with the sra command. Mothur will read the oligos files and extract the group names, or read the list of group names from the file.

Here's an example of the 2 column form with sff files:

G3BMWHG01.sff   G3BMWHG01.oligos
GHL4YHV01.sff     GHL4YHV01.oligos
GHMDAJD01.sff    GHMDAJD01.oligos
GO5715J01.sff     GO5715J01.oligos
GQY1XT001.sff    GQY1XT001.oligos
GZGO5KL01.sff    GZGO5KL01.oligos

Here is an example of the 3 column form with fastq files:

F8D0	F8D0_S345_L001_R1_001.fastq	F8D0_S345_L001_R2_001.fastq
F8D125	F8D125_S358_L001_R1_001.fastq	F8D125_S358_L001_R2_001.fastq
F8D141	F8D141_S359_L001_R1_001.fastq	F8D141_S359_L001_R2_001.fastq
F8D142	F8D142_S360_L001_R1_001.fastq	F8D142_S360_L001_R2_001.fastq
F8D143	F8D143_S361_L001_R1_001.fastq	F8D143_S361_L001_R2_001.fastq
F8D144	F8D144_S362_L001_R1_001.fastq	F8D144_S362_L001_R2_001.fastq
F8D145	F8D145_S363_L001_R1_001.fastq	F8D145_S363_L001_R2_001.fastq
F8D146	F8D146_S364_L001_R1_001.fastq	F8D146_S364_L001_R2_001.fastq
F8D147	F8D147_S365_L001_R1_001.fastq	F8D147_S365_L001_R2_001.fastq
F8D148	F8D148_S366_L001_R1_001.fastq	F8D148_S366_L001_R2_001.fastq
F8D149	F8D149_S367_L001_R1_001.fastq	F8D149_S367_L001_R2_001.fastq
F8D150	F8D150_S368_L001_R1_001.fastq	F8D150_S368_L001_R2_001.fastq
...

oligos

The oligos parameter is used to provide mothur with your oligos file. Here's a link to more information about mothur's Oligos_File.

mothur > get.mimarkspackage(oligos=GQY1XT001.oligos)

group

The group parameter is used to provide mothur with your group file. Here's a link to more information about mothur's Group_file.

mothur > get.mimarkspackage(group=final.groups)

package

The package parameter is used to select the mimarks package you would like to use. The choices are: air, host_associated, human_associated, human_gut, human_oral, human_skin, human_vaginal, microbial, miscellaneous, plant_associated, sediment, soil, wastewater or water. Default=miscellaneous. Here is a link to more information on the various packages: MIMarks_Data_Packages.

mothur > get.mimarkspackage(oligos=GQY1XT001.oligos, package=water)

requiredonly

The requiredonly parameter is used to indicate you only want the required mimarks fields printed. Default=F.

mothur > get.mimarkspackage(oligos=GQY1XT001.oligos, requiredonly=t)

Revisions

  • 1.34.0 First Introduced.
  • 1.38.1 Fixes group name issue with oligos file option so that it work with make.sra command.