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!

Questions:

  • Does it keep junk reads somewhere?

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)
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