Output Data

CSV Files

These files are found in the muri_metabarcoding/final_output/csv_output directory. All files will have the {RUN NAME} and {PRIMER} as a prefix in the file name. For example: MURI306_DL_hash_key.fasta

hash key csv	CSV file with 2 columns: DNA sequence and Hash that matches with the sequence
hash key fasta	same information as CSV file but in FASTA format (can be an input for BLAST)
ASV table	CSV with sample name, primer, hash, # of reads per sequence
taxonomy output	CSV with hash, sequence, and taxonomy assignments

RData Files

These files are found in the muri_metabarcoding/final_output/rdata_output directory. All files will have the {RUN NAME} as a prefix and {PRIMER} at the end in the file name. For example: MURI306_output_DL.Rdata

When you load this Rdata file into R, it creates the following objects in your R global environment:

cleaned.seqtab.nochim	sample name on rows and DNA sequence in columns. Frequency of each sequence per sample
freq.nochim	proportion of reads that were chimeras
track	tracking of how many reads were filtered out during each step of the script
joined_old_new_taxa	taxonomy output with hash, sequence, and taxonomy assignments
where_trim_all_Fs	where quality trimming algorithm trimmed for forward sequences
where_trim_all_Rs	where quality trimming algorithm trimmed for reverse sequences

Logs

These files are found in the muri_metabarcoding/final_output/logs directory.

tax_bootstrap.csv	taxonomy assignments (same as the taxonomy output) with the bootstrap confidence scores
cutadapt_reports	directory of reports from each sample from primer trimming using cutadapt
filtered_out_asv.csv	asv's filtered out by length after merging are saved in this csv file