Huakun-Lab / CAP-C-in-Arabidopsis

CAP-C-in-Arabidopsis

The following instructions describe the pipeline used to process Arabidopsis CAP-C libraries in the manuscript.

Dependencies and Prerequisites

The following software are required to run the Bash pipeline

• pigz
• SeqPrep
• cutadapt
• python 3.7
• HiC-Pro (>=3.0.0)

File storage structure

• 01-CAPC
  • CAPC_R1.fq.gz
  • CAPC_R2.fq.gz
• 02-cutadapt
  • CAPC_merged_001_T1.fastq.gz
  • CAPC_merged_001_T2.fastq.gz
  • CAPC_unmerged_001_A1.fastq.gz
  • CAPC_unmerged_001_G1.fastq.gz
  • CAPC_unmerged_001_A2.fastq.gz
  • CAPC_unmerged_001_G2.fastq.gz
  • ......
• 03-after_filter
  • CAPC*{OK,Short}_R1*.fastq.gz
  • CAPC*{OK,Short}_R2*.fastq.gz
• 04-fastq
  • CAPC/CAPC_merged_R1.fastq.gz
  • CAPC/CAPC_merged_R2.fastq.gz
• 20-split
  • CAPC_R1_001.fastq.gz
  • CAPC_R1_002.fastq.gz
  • ......
• 21-merge
  • CAPC_merged_001.fastq.gz
  • CAPC_unmerged_R1_001.fastq.gz
  • CAPC_unmerged_R2_001.fastq.gz
  • ......

When the Bash Script finished. You can remove folder 02-cutadapt, 03-after_filter, 20-split, 21-merge The clean fastq was storage in 04-fastq.

General Instructions to use the bash script

This bash script is used to clean the raw sequencing fastq, then you can use the clean fastq to mapping.

Step1 Split raw fastq file

Since the software SeqPrep used in the third step generally only performs single-threaded calculations, the original FASTQ files should be split into smaller FASTQ files first.

Step 2 Zip Split fastq file

In order to reduce storage usage, compress the split FASTQ files. We used pigz, which can perform multi-threaded compression on sequencing files, speeding up data processing.

Step 3 Merge R1 and R2

Use SeqPrep to merge the FASTQ reads.

Step 4 Remove Linker

Remove the linker sequences from the reads and regenerate the FASTQ files.

Step 5 Sum Split and filted

Filter the regenerated FASTQ files.

Step 6 Combine all fastq

Reassemble the filtered FASTQ files into clean FASTQ files for the next step of mapping.

After the bash script

Now we have fastq data without linkers. Then we use HiC-Pro to mapping. We provide our HiC-Pro config file CAPC_Arabidopsis_config-hicpro.txt, and use the command hicpro -i 04-fastq -o 05-rmdup_rmmulti_Seperate_HiCPro_result -c Arabidopsis_DNase_config-hicpro.txt .