aq-qualityanal.1

.\" Authors: Andre Masella
.TH aq-qualityanal 1 "October 2011" "1.2" "USER COMMANDS"
.SH NAME 
aq-qualityanal \- Produce quality statistics from Illumina reads.
.SH SYNOPSIS
.B aq-qualityanal
.SH DESCRIPTION
This calculate a number of quality statistics and produces some pretty graphs compositing all the tiles in a flow cell into a single image. The analysis will be done for any FASTQ files in the current directory when called. The ouput graphs are as follows.
.TP
\fIinput\fB.n.pdf\fR
The number of uncalled bases as distributed over the tiles.
.TP
\fIinput\fB.b.pdf\fR
The length of the quality-masked region of each read as distributed over the tiles.
.TP
\fIinput\fB.q.pdf\fR
The mean quality score as distributed over the tiles.
.TP
\fIinput\fB.cnt.pdf\fR
The number of reads as distributed over the tiles.
.TP
\fIinput\fB.qposn.pdf\fR
The average quality scores for each position in the reads.
.TP
\fIinput\fB.nposn.pdf\fR
The number of uncalled bases for each position in the reads.
.SH SEE ALSO
.BR axiome (1).