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vmaffei / dada2_to_picrust

Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)
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elemental Q regarding input seq format 'seqtab.nochim.robj' #6

Closed junhuili closed 6 years ago

junhuili commented 6 years ago

I am wondering whether the input seq format must be 'robj'. If so, how can I convert 'fasta' to 'robf'?

grab study seqs

load(file = "genome_prediction/seqtab.nochim.robj")

vmaffei commented 6 years ago

Hi junhili, .robj is required for the pipeline as written, but I am happy to write some example code for you to use a fasta. Were the sequences in the .fasta created by DADA2? If not, do you have a separate file that contains the number of times each sequence in the .fasta occurs in each sample? What software have you used up to this point?

junhuili commented 6 years ago

Hi Vince, many thanks for your prompt comments. I just tried to proceed the seq using DADA2, it works. Thank you!