josenavas
commented
7 years ago Thanks @adswafford
I've updated the Default Parameter set names as you suggested here. The only difference is this one: 100 base pairs (recommended for 16S) which I've just added 100 base pairs. The recommendation is incorrect, and it is dependent on your technology. E.g. all our recent sequencing runs are 150bp, so there is no reason to trim to 100 unless we want to do a meta-analysis with a study that has shorter reads. In general, the longer the reads the better.
The other recommendations stated in this issue (Command name changes AND specific parameter names) are not changed because those require changes on the plugins. I've moved the issue to the current development cycle.
adswafford
The dropdown text and processing parameters naming/capitalization should be improved as shown below. In addition, text in dropdown menus should be alphabetical.
Multiplexed FASTQ; generic 5 base pair barcodes Multiplexed FASTQ; generic 5 base pair barcodes with Phred quality threshold: 0 Multiplexed FASTQ; generic 5 base pair reverse complement mapping file barcodes Multiplexed FASTQ; generic 6 base pair barcodes Multiplexed FASTQ; generic 6 base pair reverse complement mapping file barcodes Multiplexed FASTQ; generic 8 base pair barcodes Multiplexed FASTQ; generic 8 base pair barcodes with Phred offset: 33 Multiplexed FASTQ; generic 8 base pair reverse complement mapping file barcodes Multiplexed FASTQ; generic 11 base pair barcodes Multiplexed FASTQ; generic 11 base pair reverse complement barcodes Multiplexed FASTQ; generic 12 base pair barcodes Multiplexed FASTQ; generic 12 base pair reverse complement barcodes Multiplexed FASTQ; Golay 12 base pair barcodes Multiplexed FASTQ; Golay 12 base pair barcodes with Phred offset: 33 Multiplexed FASTQ; Golay 12 base pair barcodes with Phred offset: 64 Multiplexed FASTQ; Golay 12 base pair reverse complement barcodes Multiplexed FASTQ; Golay 12 base pair reverse complement barcodes with Phred offset: 33 Multiplexed FASTQ; Golay 12 base pair reverse complement barcodes with Phred offset: 64 Multiplexed FASTQ; Golay 12 base pair reverse complement mapping file barcodes with reverse complement barcodes Per-sample FASTQ defaults (autodetect) Per-sample FASTQs; Phred offset: 33 (Sanger, Illumina 1.8+) Per-sample FASTQs; Phred offset: 64 (Solexa, Illumina 1.3-1.7)
Deblur (trimmed data, =<150 bp) Pick closed reference OTUs [<- this is already correct] Trim sequences (choose length below)
90 base pairs 100 base pairs (recommended for 16S) 150 base pairs 300 base pairs
Jobs to start Positive reference filtering database Threads per sample Insertion/deletion (indel) probability Negative (artifacts) filtering database Mean per nucleotide error rate Error probabilities for each Hamming distance Indexed version of the negative filtering database Sequence trim length (-1 for no trimming) An indexed version of the positive filtering database Maximum number of allowed indels Minimum study-wide read threshold Minimum per-sample read threshold