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 head
:
@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
uniq -c
them. $\endgroup$I1
$\endgroup$