know the grep command for fastq file

Question

[harry]

I have junction read sequence like this -HISEQ:151:HHKH7BCXX:2:1203:18952:80029 and i want to grep this sequence from my fastq file . so please tell me how i grep this sequence.

[brian.fristensky]

See answer at Extract specific genes from a FASTA file.

[Carambakaracho]

brian, OP asks

i want to grep this sequence from my fastq file

[brian.fristensky]

SeqKit works with both fastq and fasta files.

Answer 1

[JC]

if the file is decompressed: grep -A4 HISEQ:151:HHKH7BCXX:2:1203:18952:80029 file.fastq

if the file is compressed: zgrep -A4 HISEQ:151:HHKH7BCXX:2:1203:18952:80029 file.fastq.gz

man grep can explain to you how to use it

Answer 2

[slapiiv]

grep 'HISEQ:151:HHKH7BCXX:2:1203:18952:80029' your_fastq_file.fastq

Answer 3

[gsk1185]

grep -1 "HISEQ:151:HHKH7BCXX:2:1203:18952:80029" .fastq

[ATpoint]

Hey gsk1185, thanks for contributing but please note that exactly this answer has already been given twice. There is no point in a third identical answer.