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Mapper

cphasing mapper is designed for process Pore-C or HiFi-C data, its output two files:
(1) porec table (.porec.gz) which contain high-order contacts
(2) 4DN pairs (.pairs.gz) which only retain VPCs.

Note

The output of HiFi-C, still named .porec.gz, contains the same results whether Pore-C or HiFi-C data.

Examples#

Process one cell Pore-C data#

cphasing mapper draft.contigs.fasta sample.porec.fastq.gz -t 40

Process multiple cells Pore-C data#

Process together#

cphasing mapper draft.contigs.fasta sample1.porec.fastq.gz sample2.porec.fastq.gz -t 40
or 
cphasing mapper draft.contigs.fasta sample*.porec.fastq.gz -t 40

Note

It will output results using the sample1.porec as the prefix

Submit each cell to the cluster#

  • use multiple scripts to run mapper for each sample
    run_sample1.sh
    cphasing mapper draft.contigs.fasta sample1.porec.fastq.gz -t 40
    run_sample2.sh
    cphasing mapper draft.contigs.fasta sample2.porec.fastq.gz -t 40
    run_sample3.sh
    cphasing mapper draft.contigs.fasta sample3.porec.fastq.gz -t 40
  • merge results 
    cphasing porec-merge sample1.porec.porec.gz sample2.porec.porec.gz sample3.porec.porec.gz -o sample.merge.porec.gz
cphasing pairs-merge sample1.porec.pairs.gz sample2.porec.pairs.gz sample3.porec.pairs.gz -o sample.merge.pairs.gz

Process one cell HiFi-C data#

cphasing mapper draft.contigs.fasta sample.porec.fastq.gz -t 40 --mm2-params "-x map-hifi"

Process multiple cells HiFi-C data#

All the steps of this same with processing in the Pore-C data, with the parameter of --mm2-params "-x map-hifi".

Parameters#

cphasing mapper -h
 Usage: cphasing mapper [OPTIONS] REFERENCE FASTQ...   

 Mapper for pore-c reads.                                                  
 REFERENCE: Path of reference                                              

 FASTQ: Path of pore-c reads, multiple file enabled, the prefix of output  
 default only use sample 1.                                                

╭─ Arguments ─────────────────────────────────────────────────────────────╮
│ *  REFERENCE    (PATH) [required]                                       │
│ *  FASTQ        (PATH) [required]                                       │
╰─────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────╮
│ --enzyme        -e        Restrict site pattern, use comma to separate  │
│                           multiple patterns.                            │
│                           (STR)                                         │
│ --mm2-params              additional parameters for minimap2            │
│                           (STR)                                         │
│                           [default: -x map-ont]                         │
│ --mapq          -q        Minimum quality of mapping [0, 60].           │
│                           (INT)                                         │
│                           [default: 0; 0<=x<=60]                        │
│ --min-identity  -p        Minimum percentage identity of alignments [0, │
│                           1.0].                                         │
│                           (FLOAT)                                       │
│                           [default: 0.8; 0.0<=x<=1.0]                   │
│ --min-length    -l        Minimum length of fragments.                  │
│                           (INT)                                         │
│                           [default: 150]                                │
│ --max-edge      -me       Maximum length of fragment located in the     │
│                           edge of contigs.                              │
│                           (INT)                                         │
│                           [default: 2000]                               │
│ --force         -f        Force run all the command, ignore existing    │
│                           results. The index file also will be removed. │
│ --outprefix     -o        output prefix, if none use the prefix of      │
│                           fastq                                         │
│                           (TEXT)                                        │
│ --threads       -t        Number of threads.                            │
│                           (INT)                                         │
│                           [default: 4]                                  │
│ --help          -h,-help  Show this message and exit.                   │
╰─────────────────────────────────────────────────────────────────────────╯