Question: know the grep command for fastq file
0
gravatar for harry
5 weeks ago by
harry0
harry0 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 • 193 views
ADD COMMENTlink modified 5 weeks ago by gsk118520 • written 5 weeks ago by harry0

See answer at Extract specific genes from a FASTA file.

ADD REPLYlink written 5 weeks ago by brian.fristensky80

brian, OP asks

i want to grep this sequence from my fastq file

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Carambakaracho1.5k

SeqKit works with both fastq and fasta files.

ADD REPLYlink written 4 weeks ago by brian.fristensky80
5
gravatar for JC
5 weeks ago by
JC8.2k
Mexico
JC8.2k 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 5 weeks ago by JC8.2k
2
gravatar for slapiiv
5 weeks ago by
slapiiv40
slapiiv40 wrote:
grep 'HISEQ:151:HHKH7BCXX:2:1203:18952:80029' your_fastq_file.fastq
ADD COMMENTlink written 5 weeks ago by slapiiv40
0
gravatar for gsk1185
5 weeks ago by
gsk118520
gsk118520 wrote:

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

ADD COMMENTlink written 5 weeks 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 5 weeks ago by ATpoint21k
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