QC Files I use:

• Flowcell_QC_stats.txt- I don't usually use, it blasts reads against some ApeKI Maize and looks at read length, but only works for Maize / ApeKI
• Flowcell_QC1.txt- I use this summary table, but would like to change it a lot.
• Flowcell_QC2.txt- This has the reads per sample, very useful.
• Flowcell_adapter_dimers.txt- not too useful for me because too big of a file
• Flowcell_adapter_dimers_parsed.txt- Lists number of dimers per barcode.  I like it!
• Does it keep junk reads somewhere?

Questions:

Changes to Flowcell_QC1.txt file:

1. Can we have it write to the same file each time, just append to bottom (may need to be by enzyme)?
2. I would like to change the analysis to base it on a 96-well plate, not a lane. 
3. Fields I need (bold is most important):

• Date (not in script)
• Flowcell (not in script)
• Lane (Flowcell lane #)
• Plate Name (Currently just gives one plate if 384-plex, I'd like to do the analysis by plate)
• Read_Count (Total No of reads)
• Pass_Count (No of reads that have cut site and barcode)
• Pass_Rate (% of reads that have cut site and barcode)
• Pass_Filter_Count (No of reads that pass Illumina's filter)
• Pass_Filter_Rate (% of reads that pass Illumina's filter)
• Adapter_dimers
• N_samples (samples on plate, not including blanks)
• Mean_count (Pass_Filter_Count/n_samples)
• SD_count (std dev of mean_count, we could drop this)
• CV_count_(%) (CV of mean_count)
• No_Blanks (not in script, number of blanks on a plate)

• *Blank_Min* (not in script, for each blank, calculates Pass_count/Mean_count \[% of mean reads\], then returns the lowest value)

• *Blank_Max* (not in script, for each blank, calculates Pass_count/Mean_count \[% of mean reads\], then returns the maximum value)