Qiime Split_libraries.py Unassigned reads output not present

Question

[vincentc]

Hi,

I am trying to get unassigned reads out of my split_libraries.py command. Here is the command:

split_libraries.py \
  -f /home/vicar66/Raw_data/Nov27/fastaconvertionNov28/fasta_converted_Nov27j100.fna \
  -q /home/vicar66/Raw_data/Nov27/fastaconvertionNov28/fasta_converted_Nov27j100.qual \
  -o /home/vicar66/Raw_data/ \
  -m /home/vicar66/mapfile_vincent.txt \
  -w 50 \
  -s 30 \
  -M 2 \
  --reverse_primer_mismatches 2 \
  -H 8 \
  -l 400 \
  -L 500 \
  -a 0 \
  -b variable_length \
  -d \
  -n 1 \
  -z truncate_only \
  --retain_unassigned_reads

Even if I enable --retain_unassigned_reads, and it is mentioned in the log file that retaining unassigned reads is enabled, I only get .txt files and .fna and .qual file of my assigned reads. Anyone could help me?

Thanks!

Answer 1

[marina.v.yurieva]

--retain_unassigned_reads: retain sequences which don't map to a barcode in the mapping file (sample ID will be "Unassigned")

Probably all of them have barcode. Do you know how many should get unassigned? What is the stats in log file?