Processing Report

INPUT_FILENAME

DATESTAMP

Truncating and Mapping

  Read 1 Read 2
Total Reads INPUT_TOTAL_READS_1 INPUT_TOTAL_READS_2
Not Truncated INPUT_NOT_TRUNCATED_READ1 INPUT_NOT_TRUNCATED_READ2
Truncated INPUT_TRUNCATED_READ1 INPUT_TRUNCATED_READ2
Too short to map INPUT_TOO_SHORT_TO_MAP_READ_1 INPUT_TOO_SHORT_TO_MAP_READ_2
Average length of truncated sequence INPUT_AVERAGE_LENGTH_TRUNCATED_READ1 INPUT_AVERAGE_LENGTH_TRUNCATED_READ2
  Read 1 Read 2
Unique Alignments INPUT_UNIQUE_ALIGNMENTS_READ1 INPUT_UNIQUE_ALIGNMENTS_READ2
Multiple Alignments INPUT_MULTIPLE_ALIGNMENTS_READ1 INPUT_MULTIPLE_ALIGNMENTS_READ2
Failed To Align INPUT_FAILED_TO_ALIGN_READ1 INPUT_FAILED_TO_ALIGN_READ2
Paired INPUT_PAIRED_READ1 INPUT_PAIRED_READ2
{SONICATION_TABLE_START}

Filtering

  Di-Tag Count
Valid Pairs INPUT_VALID_PAIRS
Invalid Pairs INPUT_INVALID_PAIRS
Same Circularised INPUT_SAME_CIRCULARISED
Same Fragment Dangling Ends INPUT_SAME_DANGLING_ENDS
Same Fragment Internal INPUT_SAME_FRAGMENT_INTERNAL
Re-ligation INPUT_RE_LIGATION
Contiguous Sequence INPUT_CONTIGUOUS_SEQUENCE
Wrong Size INPUT_WRONG_SIZE
Total Pairs INPUT_TOTAL_PAIRS
{SONICATION_TABLE_END} {DOUBLE_DIGEST_TABLE_START}

Filtering

  Di-Tag Count
Valid Pairs INPUT_VALID_PAIRS
No Ligation INPUT_NO_LIGATION
Re-ligation INPUT_RE_LIGATION
Self-ligation INPUT_SELF_LIGATION
No ligation internal re2 INPUT_INTERNAL_RE2_NO_LIGATION
Unclassified INPUT_UNCLASSIFIED
Wrong size INPUT_WRONG_SIZE
Unmapped INPUT_UNMAPPED
Total Pairs INPUT_TOTAL_PAIRS
{DOUBLE_DIGEST_TABLE_END}

Di-tag length Distribution

De-duplication

Percentage uniques: INPUT_DEDUPLICATION_PERCENTAGE_UNIQUES

  All Di-Tags Unique Di-Tags
Read Pairs INPUT_DEDUPLICATION_READ_PAIRS_ALL INPUT_DEDUPLICATION_READ_PAIRS_UNIQUES
Cis-close (< 10Kbp) INPUT_DEDUPLICATION_CIS_CLOSE_ALL INPUT_DEDUPLICATION_CIS_CLOSE_UNIQUES
Cis-far (> 10Kbp) INPUT_DEDUPLICATION_CIS_FAR_ALL INPUT_DEDUPLICATION_CIS_FAR_UNIQUES
Trans INPUT_DEDUPLICATION_TRANS_ALL INPUT_DEDUPLICATION_TRANS_UNIQUES