fastq.info

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

file

The file lines can be 2, 3, or 4 columns. The forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file, or forward fastq file then reverse fastq then forward index and reverse index file. If you only have one index file add ‘none’ for the other one.

Two Column

ffastqfile1 rfastqfile1
ffastqfile2 rfastqfile2
...

Two Column PacBio

group1 pacBioFastqfile1
group2 pacBioFastqfile2
group3 pacBioFastqfile3
...

Three Column

group ffastqfile  rfastqfile
group ffastqfile  rfastqfile
group ffastqfile  rfastqfile
...

Four Column  - ('none' is the option for no forward index file)

My.forward.fastq My.reverse.fastq none My.rindex.fastq


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.