Question: Read detection with pattern in paired end FASTQ file
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amitpande74 • 10 wrote:
HI,
I have paired end reads, and want to extract reads which have the insert TGTATGTAAACTTCCGACTTCAACTGTAin them.
I tried with grep -A2 -B1 "TGTATGTAAACTTCCGACTTCAACTGTA" input.fq |grep -v "^\-\-$" > 1.fq and 2.fq
But they dont align with Bowtie2 anymore, because the reads have differing headers.
I even tried using bbduk.sh in1=input_1.fq in2=input_2.fq out1=matched_1.fq out2=matched_2.fq k=28 literal=TGTATGTAAACTTCCGACTTCAACTGTA rcomp=f but it is of no avail.
Can someone help.
Regards.
