extract barcode from a fastq file

Question

[najibveto]

hello, sorry for disturbing. i would like to know how to extract barcode from a fastq file. my fastq file is as follow;

thank you for your help.

[cpad0112]

seqkit seq -n input.fastq.gz | awk -F ":" '{print $NF}' | awk '!a[$1]++'

[najibveto]

thank you for your help.

Answer 1

[h.mon]

Assuming you are talking about Illumina barcodes, you can extract them from the header lines:

zcat file.fastq.gz \
  | awk 'NR%4==1' \
  | awk -F":" '{print $(NF)}' \
  | sort \
  | uniq -c

As others pointed out, you didn't provide information enough, and using pictures to illustrate text isn't a good practice.

[najibveto]

thank you for your reply. sorry next time I will provide a text file and more information.

[lkianmehr]

How about ion torrent platform?