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know the grep command for fastq file

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.

rna-seq
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updated by gsk1185 • gsk1185 • written by harry • harry

brian, OP asks

i want to grep this sequence from my fastq file

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written by Carambakaracho Carambakaracho

SeqKit works with both fastq and fasta files.

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written by brian.fristensky brian.fristensky

3 answers

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

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written by JC JC 
grep 'HISEQ:151:HHKH7BCXX:2:1203:18952:80029' your_fastq_file.fastq
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written by slapiiv • slapiiv

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

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written by gsk1185 • gsk1185

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.

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written by ATpoint ATpoint

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