All my reads in fastq files are supposed to have custom index sequences at 5th nucleotide from 5' end.
(for example, 5' NNNN-IndexSeq-restReadSequences)
I tried to demultiplexed them with several tools on the web, but I couldn't get consistent results from those tools.
For just "sanity check", I want to actually count or extract indexed reads with simple shell commands.
I'm not sure if I'm saying right, but most tools search indexes in the whole reads, but I want to look for indexes at specific position (i.e. 5th - 9th nucleotides).
I hope you guys could understand my poor English.