软件介绍
HiCUP是一个处理由Hi-C和捕获Hi-C（Capture Hi-C，CHi-C）产生的测序数据的流程，用于对HiC数据进行质控（QC）并得到报告。
hicup.png
软件的安装
conda install hicup -y
软件的使用
step1 构建一个contig文件或基因组文件的bowtie索引（index）
#用bowtie2-build构建fasta文件的index
bowtie2-build 9204.contig.fasta 9204.contig.fasta
step2使用内置脚本hicup_digester在参考序列上寻找酶切位点，生成酶切信息文件
hicup_digester --re1 ^GATC,DpnII --genome 9201_digester_db 9201.contigs.fasta
note
--re1 or --re2 #选择内切酶，根据自己hic数据使用的限制性内切酶，进行选择：A^GATCT,BglII A^AGCTT,HindIII ^GATC,DpnII
--genome 这个参数后面添加的是输出文件的名称，且必须按照prefix_digester_db进行命名，不然运行不成功
9201.contigs.fasta 就是你的参考序列了
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#生成的酶切信息文件
Digest_9201_digester_db_DpnII_None_09-46-31_17-08-2023.txt
step3 编写配置文件---hicup_example.conf
hicup --example
#生成hicup_example.conf的配置文件
$cat hicup_example.conf
#Example configuration file for the hicup Perl script - edit as required
########################################################################
#Directory to which output files should be written (optional parameter)
#Set to current working directory by default
Outdir:#默认就行
#Number of threads to use
Threads: 40 ##设置线程数
#Suppress progress updates (0: off, 1: on)
Quiet:0#默认就行
#Retain intermediate pipeline files (0: off, 1: on)
Keep:0#默认就行
#Compress outputfiles (0: off, 1: on)
Zip:1#默认就行
#Path to the alignment program (Bowtie or Bowtie2)
#Remember to include the executable Bowtie/Bowtie2 filename.
#Note: ensure you specify the correct aligner i.e. Bowtie when
#using Bowtie indices, or Bowtie2 when using Bowtie2 indices.
#In the example below Bowtie2 is specified.
Bowtie2: /share/home/off/biosoft/bowtie2-2.4.1-linux-x86_64/bowtie2#设置自己的bowtie2的路径
#Path to the reference genome indices
#Remember to include the basename of the genome indices
Index: /share/home/off/Work/Genome/01.hic_tmp/9201/9201.contigs#设置bowtie2构建的索引文件位置
#Path to the genome digest file produced by hicup_digester
/share/home/off/Work/Genome_assembly/01.hic_tmp/9201/Digest_9201_digester_db_DpnII_None_09-46-31_17-08-2023.txt#hicup_digester生成的酶切信息文件
#FASTQ format (valid formats: 'Sanger', 'Solexa_Illumina_1.0', 'Illumina_1.3' or 'Illumina_1.5')
#If not specified, HiCUP will try to determine the format automatically by analysing
#one of the FASTQ files. All input FASTQ will assumed to be in this format
Format: Sanger#默认就行
#Maximum di-tag length (optional parameter)
Longest: 800#默认就行
#Minimum di-tag length (optional parameter)
Shortest: 150#默认就行
#FASTQ files to be analysed, placing paired files on adjacent lines\
#设置需要质控的HiC数据
/share/home/off_wenhao/Work/Genome_assembly/01.hic_tmp/9201/9201_S38_L001_R1_001.fastq.gz
/share/home/off_wenhao/Work/Genome_assembly/01.hic_tmp/9201/9201_S38_L001_R2_001.fastq.gz
step4 运行程序
hicup --config hicup_example.conf
or
hicup --bowtie2 /share/home/off/biosoft/bowtie2-2.4.1-linux-x86_64/bowtie2\
--digest/share/home/off/Work/Genome/01.hic_tmp/9201/Digest_9201_digester_db_DpnII_None_09-46-31_17-08-2023.txt\
--format Sanger\
--index /share/home/off/Work/Genome_assembly/01.hic_tmp/9201/9201.contigs\
--keep \
--outdir /path/to/output/dir \
--threads 40 \
/path/to/reads*.fastq.gz
结果文件
hic-perfix.fastq.gz.truncation_barchart.svg
hic-perfix.trunc.fastq.gz.mapper_barchart.svg
hic-perfix.ditag_size_distribution.svg
hic-perfix.filt.bam.deduplicator_cis_trans_piechart.svg
hic-perfix.filt.bam.deduplicator_uniques_barchart.svg
hic-perfix.pair.bam.filter_piechart.svg
hic-perfix.fastq.gz.truncation_barchart.svg
hic-perfix.trunc.fastq.gz.mapper_barchart.svg
还有很多txt的文件，可以进行查看
参考链接
https://www.bioinformatics.babraham.ac.uk/projects/hicup/
//www.greatytc.com/p/61899b60ef63
