--minimum_length with default value 15, the output fastq file also contained length 0 read.
command:
iCount demultiplex hnRNPC.fq.gz AGATCGGAAGAGCGGTTCAG NNNGGTTNN NNNTTGTNN
NNNCAATNN NNNACCTNN NNNGGCGNN --out_dir "demultiplexed"
result:
Thanks for your time and all the best,
Iris