Statistics file

The statistics file (*.stats.json) contains detailed statistics relating to the counts.

Data fields

These fields concern execution, options and the raw input data:

• command
  • Command executed to generate this file
• version
  • Version of pyCROQUET used to generate this file
• sample_name
  • Sample as determined from command or from BAM/CRAM header
• reversed_reads
  • Reads were reversed before attempting counts
• total_guides
  • Total number of guides in library
• total_reads
  • Total number of reads in input data
• total_pairs
  • When dual guide, number of read pairs

Filter related fields

Fields that indicate volume of data excluded for various reasons:

• length_excluded_reads
  • Number of reads excluded due to minimum length not being achieved
• vendor_failed_reads
  • Number of reads excluded due to vendor failed flag (when selected)

Read count fields

• mapped_to_guide_reads
  • Number of reads mapped to a guide
• multimap_reads
  • Number of reads mapping to multiple guides equally well
• unmapped_reads
  • Number of reads failing to map to a guide

Guide count fields

• low_count_guides_lt_15
  • Number of guides with less-than 15 reads
• low_count_guides_lt_30
  • Number of guides with less-than 30 reads
• low_count_guides_user
  • User definable threshold, when active contains a structure of {"count": 101064, "lt": 5}
• mean_count_per_guide
  • Mean reads per guide
• zero_count_guides
  • Number of guides with zero reads

pair_classifications

Pair classification is only defined for dual-guide mode. Details can be found here.

merged_from

The complete statistics from files merged together are incorporated into this field in an array matching the order in the header for the *.counts.tsv.gz.

Example can be seen here.