https://wiki.anunna.wur.nl/index.php?action=history&feed=atom&title=Command_line_tricks_for_manipulating_fastqCommand line tricks for manipulating fastq - Revision history2026-04-18T17:38:29ZRevision history for this page on the wikiMediaWiki 1.43.1https://wiki.anunna.wur.nl/index.php?title=Command_line_tricks_for_manipulating_fastq&diff=816&oldid=prevMegen002: Created page with "== Extracting a sequence based on read name == <source lang='bash'> gunzip -c reads.fq.gz | sed -n '/readname/,+3 p' </source> == From BAM/SAM to fastq == <source lang='bas..."2013-12-08T11:25:44Z<p>Created page with "== Extracting a sequence based on read name == <source lang='bash'> gunzip -c reads.fq.gz | sed -n '/readname/,+3 p' </source> == From BAM/SAM to fastq == <source lang='bas..."</p>
<p><b>New page</b></p><div>== Extracting a sequence based on read name ==<br />
<br />
<source lang='bash'><br />
gunzip -c reads.fq.gz | sed -n '/readname/,+3 p'<br />
</source><br />
<br />
== From BAM/SAM to fastq ==<br />
<br />
<source lang='bash'><br />
samtools view bamfile.bam | grep -v '^@' | awk '{print "@"$1"\n"$10"\n+\n"$11}'<br />
</source><br />
<br />
== From fastq to fasta ==<br />
<source lang='bash'><br />
gunzip -c fastqfile.fq.gz | sed 's/^@/>/' | awk '{print;getline;print;getline;getline}' <br />
</source><br />
<br />
== Counting number of bases in a fastq file ==<br />
<source lang='bash'><br />
gunzip -c fastqfile.fq.gz | awk '{;getline;print;getline;getline}' | wc<br />
</source></div>Megen002