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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.
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(file=fastqFiles.file)
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).
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.
The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.
The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.
When pacbio is set to true, quality scores of 0 will results in a corresponding base of N. Default=F.
The format parameter is used to indicate whether your sequences are sanger, solexa, illumina or illumina1.8+. default=sanger.
- 1.24.0 Added fasta and qfile options. - http://www.mothur.org/forum/viewtopic.php?f=5&t=1444
- 1.28.0 Added format option
- 1.28.0 Fixed negative quality scores related to format of sequences. - http://www.mothur.org/forum/viewtopic.php?f=4&t=1727&p=4651&hilit=fastq.info#p4651
- 1.30.0 added illumina1.8+ format.
- 1.30.0 added pacbio parameter.