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.

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