Editing BioMicroCenter:IlluminaDataPipeline (section)

=== Summary.htm ===
The ''Summary.htm'' file is the basic quality control file associated with your run. The information in the lane results summary section is the best place to begin. The key pieces of informaiton are:
* Clusters (raw): The number of clusters detected by the image analysis module of the Pipeline software
* Clusters (PF): The number of clusters detected that meet the filtering parameters. These filtering parameters are adjustable *** add info on filtering parameters ***
* % Align (PF): The percentage of filtered reads that were uniquely aligned to the reference genome.
* % Error Rate (PF): The percentage of called bases in aligned reads that do not match the reference. This does not mean the base calls are incorrect, simply that they are not aligned.

Note that the intensity scores have lost most of their utility with the 1.3.2 Pipeline software.w

If you are running a ''paired end'' run, some additional parameters are useful further down.
* Relative orientation statistics. Here, you want to look at the ''>'' and ''<'' signs. "><" reads are pointing to each other while all other configurations (<<,>>,<>) suggest some type of rearangement has caused the reads to point either in parallel or become divergent. 
* Insert statistics: The software calculates the median insert size (of the >< reads) and the std. deviation. The software then calculates out reads that are statistically too large or too small to be expected from the distribution. these reads have the possibility of representing IN/DEL regions.
*'''Reads that fail these thresholds are reported in the s_N_anomaly.txt file'''

	We will be working on additional QC metrics that can be reported in the coming months.