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Difference between revisions of "Fastq.info"

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The fastq.info command reads a fastq file and creates a fasta and quality file.
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The fastq.info command reads a fastq file and creates a fasta and quality file or can be used to parse fastq files by sample.
 
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==Default settings==
 
==Default settings==
The fastq.info command parameters are fastq, fasta and qfilefastq is required.
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The fastq.info command parameters are file, fastq, fasta, qfile, oligos, group and format; file or fastq is required.
  
 
  mothur > fastq.info(fastq=M11Fcsw.fastq)
 
  mothur > fastq.info(fastq=M11Fcsw.fastq)
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or
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mothur > fastq.info(file=fastqFiles.file)
  
 
==Options==
 
==Options==
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===oligos===
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The oligos parameter allows you to provide an oligos file to split your fastq file into separate fastq files by barcode and primers.
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===bdiffs & pdiffs & ldiffs & sdiffs & tdiffs===
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These parameters are used to allow differences in the barcode, primers, linkers and spacers. pdiffs is maximum number of differences to the primer sequence, default=0. bdiffs is maximum number of differences to the barcode sequence, default=0.  ldiffs is maximum number of differences to the linker sequence, default=0. sdiffs is maximum number of differences to the spacer sequence, default=0. tdiffs is maximum total number of differences to the barcode, primer, linker and spacer (default to pdiffs + bdiffs + ldiffs + sdiffs).
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===checkorient===
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If you are running the fastq.info command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment.
  
 
===fasta===
 
===fasta===

Revision as of 17:00, 25 September 2015

The fastq.info command reads a fastq file and creates a fasta and quality file or can be used to parse fastq files by sample.

Default settings

The fastq.info command parameters are file, fastq, fasta, qfile, oligos, group and format; file or fastq is required.

mothur > fastq.info(fastq=M11Fcsw.fastq)

or

mothur > fastq.info(file=fastqFiles.file)

Options

oligos

The oligos parameter allows you to provide an oligos file to split your fastq file into separate fastq files by barcode and primers.

bdiffs & pdiffs & ldiffs & sdiffs & tdiffs

These parameters are used to allow differences in the barcode, primers, linkers and spacers. pdiffs is maximum number of differences to the primer sequence, default=0. bdiffs is maximum number of differences to the barcode sequence, default=0. ldiffs is maximum number of differences to the linker sequence, default=0. sdiffs is maximum number of differences to the spacer sequence, default=0. tdiffs is maximum total number of differences to the barcode, primer, linker and spacer (default to pdiffs + bdiffs + ldiffs + sdiffs).

checkorient

If you are running the fastq.info command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment.

fasta

The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.

qfile

The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.

pacbio

When pacbio is set to true, quality scores of 0 will results in a corresponding base of N. Default=F.

format

The format parameter is used to indicate whether your sequences are sanger, solexa, illumina or illumina1.8+. default=sanger.

Revisions