hicstuff

note

Hi-C pipeline that generates contact maps from sequencing reads.

https://github.com/koszullab/hicstuff

The module parses two file types from the hicstuff Hi-C pipeline:

• Pipeline log files (*.log, *.txt), identified by the ## hicstuff: header line. The end-of-run summary stats dictionary feeds the General Statistics table and the Read Fate stacked bar plot.
• Distance law tables (default distance_law.txt, also commonly seen with .tsv extensions), identified by a ## distance_law header. These drive the P(s) contact-probability line graph and its log-log slope plot.

hicstuff writes a summary stats dictionary to the log at the end of each run:

## hicstuff: v3.2.2 log file
## date: 2024-02-16 14:00:23
## enzyme: DpnII,HinfI
## input1: ../tinyMapper/tests/testHiC_R1.fq.gz
## input2: ../tinyMapper/tests/testHiC_R2.fq.gz
## ref: /home/rsg/genomes/S288c/S288c.fa
---
...
2024-02-16,14:00:43 :: INFO :: 77% reads (single ends) mapped with Q >= 30 (154272/200000)
2024-02-16,14:00:44 :: INFO :: 66943 pairs successfully mapped (66.94%)
2024-02-16,14:00:46 :: INFO :: Fetching mapping and pairing stats
2024-02-16,14:00:46 :: INFO :: {'Sample': 'testHiC^CGNT57', 'Total read pairs': 100000, 'Mapped reads': 154272, 'Unmapped reads': 45728, 'Recovered contacts': 66943, 'Final contacts': 66943, 'Removed contacts': 0, 'Filtered out': 0, 'Loops': 0, 'Uncuts': 0, 'Weirds': 0, 'PCR duplicates': 0}
2024-02-16,14:00:46 :: INFO :: Contact map generated after 0h 0m 23s

File search patterns

hicstuff/distancelaw:
  contents: '## distance_law'
  num_lines: 5
hicstuff/pipeline_stats:
- contents: '## hicstuff:'
  fn: '*.txt'
  num_lines: 100
- contents: '## hicstuff:'
  fn: '*.log'
  num_lines: 10