HiC Mapper¶

one cell¶

cphasing hic mapper -f draft.asm.fasta -1 hic_R1.fastq.gz -2 hic_R2.fastq.gz -t 40

Note

If the total length of your input genome is larger than 8 Gb, the -k 27 -w 14 should be specified, to avoid the error of chromap.

Note

By default, cphasing hic mapper uses _chromap (the modified version in C-Phasing) as the aligner. You can specify different aligners using the -a or --aligner option:

_chromap (default): Modified version of Chromap bundled with C-Phasing.
chromap: Official version of Chromap.
bwa-mem2: High-performance BWA MEM.
minibwa: A faster bwa aligner.

mutiple cells¶

Submit by specified multiple times¶

run_mapping.sh

cphasing hic mapper -f draft.asm.fasta -1 hic-1_R1.fastq.gz -1 hic-2_R1.fastq.gz -2 hic-1_R2.fastq.gz -2 hic-2_R2.fastq.gz -t 40

Note

The input Hi-C reads must paired by position

Submit each cell to the cluster¶

use multiple scripts to run mapper for each sample

run_sample1.sh

cphasing hic mapper -f draft.asm.fasta -1 hic-1_R1.fastq.gz -2 hic-1_R2.fastq.gz -t 40

run_sample2.sh

cphasing hic mapper -f draft.asm.fasta -1 hic-2_R1.fastq.gz -2 hic-2_R2.fastq.gz -t 40

run_sample3.sh

cphasing hic mapper -f draft.asm.fasta -1 hic-3_R1.fastq.gz -2 hic-3_R2.fastq.gz -t 40

Note

Please submit one first; wait until the index is successfully created and the remaining jobs are enabled to submit to the cluster.

merge results

cphasing pairs-merge hic-*.pairs.pqs -o hic.merge.pairs.pqs