I recently did some sequencing on a MiniSeq and unexpectedly the
Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I would like to know which indices are present in this file and ideally get a frequency of all index sequences in this file. How can I do this?
This is the output of
@MN00148:128:000H2YCW2:1:11102:12116:1065 1:N:0:0 GNAGAGGATTCAGGGAGCCAGCGCGCATATATCAG + F#FFFFFFFFFFFFFFFFFFA=/A/////////// @MN00148:128:000H2YCW2:1:11102:11354:1065 1:N:0:0 GNACCCGTGCGGCTGGAGAGACCACTAGAAAGAAT + A#AFFFFFFFFFFFFFFFFF///////FF=////6 @MN00148:128:000H2YCW2:1:11102:4103:1066 1:N:0:0 ANGTTGGTGGTACATCAGGGACGCGGAGATCTCAG