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Difference between revisions of "Fastq.info"
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Two Column PacBio
Two Column PacBio
Revision as of 20:22, 30 September 2019
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 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
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.
- 1.42.0 Adds Oligos class and split.groups commands fastq.info. #499
- 1.43.0 Adds 2 column pacbio file option to fastq.info. #649