sub.sample quality file


Would it be possible to include the quality file as an option in the sub.sample command?
I currently have huge HiSeq datasets and it would be amazing if in the future this option would be available for extracting small proportions of the fasta & quality file to optimize my pipeline before running the real datasets.


If you’re on a linux computer you could do something like…

head -n 40000 my.fastq > my.subsample.fastq

You’d run this from the command prompt (not in mothur) and it would return the first 10000 sequences from your fastq file and put them in a file called my.subsample.fastq.


that helped!