qiime version 1.9.1
R1=seqs.fq
R2=R2R3.paired.fq
split_libraries_fastq.py -i $R1 -o ./mismatach_0 -b $R2 -m ./edited_mapping_file.txt --max_barcode_errors 0 --sequence_max_n 0 --phred_quality_threshold 20 --max_bad_run_length 300 --min_per_read_length_fraction 0.75 --barcode_type 16
Sequences generated: 44233728
split_libraries_fastq.py -i $R1 -o ./mismatach_1 -b $R2 -m ./edited_mapping_file.txt --max_barcode_errors 1 --sequence_max_n 0 --phred_quality_threshold 20 --max_bad_run_length 300 --min_per_read_length_fraction 0.75 --barcode_type 16
Sequences generated: 44233728
split_libraries_fastq.py -i $R1 -o ./mismatach_2 -b $R2 -m ./edited_mapping_file.txt --max_barcode_errors 2 --sequence_max_n 0 --phred_quality_threshold 20 --max_bad_run_length 300 --min_per_read_length_fraction 0.75 --barcode_type 16
Sequences generated: 44233728
I get exact same logs for all three runs. It is as following:
Total number of input sequences: 91697563
Barcode not in mapping file: 44642128
Read too short after quality truncation: 2813038
Count of N characters exceeds limit: 8669
Illumina quality digit = 0: 0
Barcode errors exceed max: 0
I don't know what is going wrong. I was expecting difference in output for sequence counts and similar changes in logs.
Kindly help me through this.
--retain_unassigned_reads
Retain sequences which don ’t map to a barcode in the mapping file (sample ID will be “Unassigned”) [default: False]