General Information
File: <%=obj@filename%>
Type: FASTQ
Sequence Length Range: <%=sl.range[1]%> to <%=sl.range[2]%>
Total Sequences: <%=sum(obj@seq.lengths)%>
Unique Sequences: <%=length(obj@hash)%>
Quality by Position
<%
png(file.path(dir, 'images', 'qualplot.png'), width=WIDTH)
plotQuals(obj)
dev.off()
%>
Grey lines: 10% and 90% quantiles
Orange lines: 25% and 75% quartiles
Blue point: median
Green dash: mean
Purple line: lowess curve
Nucleotide Frequency by Position
<%
png(file.path(dir, 'images', 'basefreqs.png'), width=WIDTH, height=HEIGHT)
plotBases(obj)
dev.off()
%>
Nucleotide Proportion by Position
<%
png(file.path(dir, 'images', 'baseprops.png'), width=WIDTH, height=HEIGHT)
plotBases(obj, type="prop")
dev.off()
%>
N Frequency by Position
<%
png(file.path(dir, 'images', 'nfreq.png'), width=WIDTH, height=HEIGHT)
plotBases(obj, bases='N')
dev.off()
%>
GC Content by Position
<%
png(file.path(dir, 'images', 'gc.png'), width=WIDTH, height=HEIGHT)
plotGC(obj)
dev.off()
%>
Sequence Length Distribution
<%
png(file.path(dir, 'images', 'seqlengths.png'), width=WIDTH, height=HEIGHT)
plotSeqLengths(obj)
dev.off()
%>
Most Frequent Sequences
<%
if (obj@hashed) {
x <- makeHashTable(obj)
print(x, type="html")
} else {
cat("No sequence frequency information available - readSeqFile() run with hash=FALSE")
}
%>
Report produced by the R package qrqc