http://amos.sourceforge.net/wiki/index.php?action=history&feed=atom&title=FastqQC
FastqQC - Revision history
2026-04-30T08:27:32Z
Revision history for this page on the wiki
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http://amos.sourceforge.net/wiki/index.php?title=FastqQC&diff=252&oldid=prev
Mcschatz at 19:34, 17 May 2010
2010-05-17T19:34:34Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 19:34, 17 May 2010</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 26:</td>
<td colspan="2" class="diff-lineno">Line 26:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>qc2name=paste(dir, qc2pre,"_sequence.txt.qc", sep="")</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>qc2name=paste(dir, qc2pre,"_sequence.txt.qc", sep="")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>qc2 <- read.table(qc2name, header=TRUE)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>qc2 <- read.table(qc2name, header=TRUE)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">len<-dim(qc1)[1]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>plot(qc1$pos, qc1$X.A, type="l", col="red", ylim=c(0,40), xlab="", ylab="", main=qc1pre, axes=FALSE, frame.plot=TRUE)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>plot(qc1$pos, qc1$X.A, type="l", col="red", ylim=c(0,40), xlab="", ylab="", main=qc1pre, axes=FALSE, frame.plot=TRUE)</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 33:</td>
<td colspan="2" class="diff-lineno">Line 35:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc1$pos, qc1$X.N, col="black")</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc1$pos, qc1$X.N, col="black")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc1$pos, qc1$Q, col="purple", lty=2)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc1$pos, qc1$Q, col="purple", lty=2)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>abline(v=seq(0,<del class="diffchange diffchange-inline">80</del>,10), col="grey", lty=3)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>abline(v=seq(0,<ins class="diffchange diffchange-inline">len</ins>,10), col="grey", lty=3)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>abline(h=seq(0,<del class="diffchange diffchange-inline">80</del>,10), col="grey", lty=3)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>abline(h=seq(0,<ins class="diffchange diffchange-inline">len</ins>,10), col="grey", lty=3)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>axis(side=1, at=seq(0,<del class="diffchange diffchange-inline">80</del>,by=10))</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>axis(side=1, at=seq(0,<ins class="diffchange diffchange-inline">len</ins>,by=10))</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>axis(side=2, at=seq(0,<del class="diffchange diffchange-inline">80</del>,by=10))</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>axis(side=2, at=seq(0,<ins class="diffchange diffchange-inline">len</ins>,by=10))</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>plot(qc2$pos, qc2$X.A, type="l", col="red", ylim=c(0,40), xlab="", ylab="", main=qc2pre, frame.plot=TRUE)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>plot(qc2$pos, qc2$X.A, type="l", col="red", ylim=c(0,40), xlab="", ylab="", main=qc2pre, frame.plot=TRUE)</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 44:</td>
<td colspan="2" class="diff-lineno">Line 46:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc2$pos, qc2$X.N, col="black")</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc2$pos, qc2$X.N, col="black")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc2$pos, qc2$Q, col="purple", lty=2)</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>lines(qc2$pos, qc2$Q, col="purple", lty=2)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>abline(v=seq(0,<del class="diffchange diffchange-inline">80</del>,10), col="grey", lty=3)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>abline(v=seq(0,<ins class="diffchange diffchange-inline">len</ins>,10), col="grey", lty=3)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>abline(h=seq(0,<del class="diffchange diffchange-inline">80</del>,10), col="grey", lty=3)</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>abline(h=seq(0,<ins class="diffchange diffchange-inline">len</ins>,10), col="grey", lty=3)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>axis(side=1, at=seq(0,<del class="diffchange diffchange-inline">80</del>,by=10))</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>axis(side=1, at=seq(0,<ins class="diffchange diffchange-inline">len</ins>,by=10))</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>axis(side=2, at=seq(0,<del class="diffchange diffchange-inline">80</del>,by=10))</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>axis(side=2, at=seq(0,<ins class="diffchange diffchange-inline">len</ins>,by=10))</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>dev.off()</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>dev.off()</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div></pre></div></td></tr>
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Mcschatz
http://amos.sourceforge.net/wiki/index.php?title=FastqQC&diff=236&oldid=prev
Mcschatz: Created page with 'Quality check a fastq for position dependent sequencing or quality biases Example fastqqc.pl -tsv file.fq > file.fq.qc File:Fastqqc.png == FastqQC Plot == <pre> ## R …'
2009-11-30T18:56:34Z
<p>Created page with 'Quality check a fastq for position dependent sequencing or quality biases Example fastqqc.pl -tsv file.fq > file.fq.qc <a href="/wiki/index.php/File:Fastqqc.png" title="File:Fastqqc.png">File:Fastqqc.png</a> == FastqQC Plot == <pre> ## R …'</p>
<p><b>New page</b></p><div>Quality check a fastq for position dependent sequencing or quality biases<br />
<br />
Example<br />
fastqqc.pl -tsv file.fq > file.fq.qc<br />
<br />
<br />
[[File:Fastqqc.png]]<br />
<br />
<br />
== FastqQC Plot ==<br />
<br />
<pre><br />
## R script for generating quality plot<br />
## Shows the per position sequence composition (A=red, T=orange, G=green, C=cyan, N=black)<br />
## And the per position average quality value (dashed-purple line)<br />
prefix="s_7"<br />
dir="./"<br />
<br />
pdf(paste(paste(dir,prefix,sep=""),".qc.pdf",sep=""))<br />
par(mfrow=c(2,1))<br />
<br />
qc1pre = paste(prefix,"_1", sep="")<br />
qc1name=paste(dir, qc1pre,"_sequence.txt.qc", sep="")<br />
qc1 <- read.table(qc1name, header=TRUE)<br />
qc2pre = paste(prefix,"_2", sep="")<br />
qc2name=paste(dir, qc2pre,"_sequence.txt.qc", sep="")<br />
qc2 <- read.table(qc2name, header=TRUE)<br />
<br />
plot(qc1$pos, qc1$X.A, type="l", col="red", ylim=c(0,40), xlab="", ylab="", main=qc1pre, axes=FALSE, frame.plot=TRUE)<br />
lines(qc1$pos, qc1$X.C, col="cyan")<br />
lines(qc1$pos, qc1$X.G, col="green")<br />
lines(qc1$pos, qc1$X.T, col="orange")<br />
lines(qc1$pos, qc1$X.N, col="black")<br />
lines(qc1$pos, qc1$Q, col="purple", lty=2)<br />
abline(v=seq(0,80,10), col="grey", lty=3)<br />
abline(h=seq(0,80,10), col="grey", lty=3)<br />
axis(side=1, at=seq(0,80,by=10))<br />
axis(side=2, at=seq(0,80,by=10))<br />
<br />
plot(qc2$pos, qc2$X.A, type="l", col="red", ylim=c(0,40), xlab="", ylab="", main=qc2pre, frame.plot=TRUE)<br />
lines(qc2$pos, qc2$X.C, col="cyan")<br />
lines(qc2$pos, qc2$X.G, col="green")<br />
lines(qc2$pos, qc2$X.T, col="orange")<br />
lines(qc2$pos, qc2$X.N, col="black")<br />
lines(qc2$pos, qc2$Q, col="purple", lty=2)<br />
abline(v=seq(0,80,10), col="grey", lty=3)<br />
abline(h=seq(0,80,10), col="grey", lty=3)<br />
axis(side=1, at=seq(0,80,by=10))<br />
axis(side=2, at=seq(0,80,by=10))<br />
<br />
dev.off()<br />
</pre></div>
Mcschatz