Question: know the grep command for fastq file
0
gravatar for harry
11 months ago by
harry10
harry10 wrote:

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 • 452 views
ADD COMMENTlink modified 11 months ago by gsk118520 • written 11 months ago by harry10

See answer at Extract specific genes from a FASTA file.

ADD REPLYlink written 11 months ago by brian.fristensky90

brian, OP asks

i want to grep this sequence from my fastq file

ADD REPLYlink modified 11 months ago • written 11 months ago by Carambakaracho2.2k

SeqKit works with both fastq and fasta files.

ADD REPLYlink written 11 months ago by brian.fristensky90
5
gravatar for JC
11 months ago by
JC10k
Mexico
JC10k wrote:

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

ADD COMMENTlink written 11 months ago by JC10k
2
gravatar for slapiiv
11 months ago by
slapiiv50
slapiiv50 wrote:
grep 'HISEQ:151:HHKH7BCXX:2:1203:18952:80029' your_fastq_file.fastq
ADD COMMENTlink written 11 months ago by slapiiv50
0
gravatar for gsk1185
11 months ago by
gsk118520
gsk118520 wrote:

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

ADD COMMENTlink written 11 months ago by gsk118520

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.

ADD REPLYlink written 11 months ago by ATpoint36k
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