mothur

Fastq.info with oligos-file

I have a fastq-file that contains all samples in the given sequencing run. I need to split the file by sample to get separate fastq files for each sample. I tried to run following command:

fastq.info(fastq=libA_S1_L001_R1_001.fastq, oligos=oligos.oligos, format=illumina1.8+)

The command ran 1 hour and then I canceled it because it was producing only five files (scrap.qual, scrap.fastq, scrap.fasta, qual and fasta) all with file name starting with libA_S1_L001_R1_001. Is this how the command should work or is there something wrong? Wiki page says: “The oligos parameter allows you to provide an oligos file to split your fastq file into separate fastq files by barcode and primers. “ So I thought fastq.info would produce separate fastq-files for each sample. If this command does not do it, is there any other direct way to do this in mothur? I know how to do this with a complicated and time consuming way (running make.contigs with oligos option and then get.groups, list.seqs and get.seqs for each sample), but it would be great to find a quicker way to do this!

Are you running our current version? https://github.com/mothur/mothur/releases/tag/v.1.43.0

Is the libA_S1_L001_R1_001.fastq file the forward fastq file from a pair? If so, try this:

myFastq.file:
libA_S1_L001_R1_001.fastq libA_S1_L001_R2_001.fastq

mothur > fastq.info(file=myFastq.file, oligos=oligos.oligos, format=illumina1.8+, pdiffs=2, bdiffs=1) - this should create a fastq file for each sample as well as a group file.

Thank you so much for the solution, now it worked! Of course I should have realized I need to give both file names…

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