HIC Pro | HIC data processing tool

One 、HiC-Pro

1. HiC-Pro Official website

https://github.com/nservant/HiC-Pro

2. Download the package

git clone https://github.com/nservant/HiC-Pro.git

3. utilize conda Configure the software running environment

conda env create -n hicpro -f /gss1/home/tri01/software/HiC-Pro/environment.yml

4. HiC-Pro Build and install

 modify config-install.txt and config-system.txt The path under the file 
make configure
make install

Two 、 Operation document preparation

5. Prepare three documents ：bed、table、bowtie2 Built index ,bed、table File format can refer to HiC-Pro Software installation package annotation List of human and mouse .bed and .sizes file .
   bed The file is made up of the fasta file , after digest_genome.py Of python Script processing results in , The specific command is ：python digest_genome.py -r ^GATC -o Tden_mobi.bed Tden.genome.fasta.
   Index file utilization bowtie2 obtain , The specific command is ： bowtie2-build Tchi.fasta tc
   # first Tchi.fasta Represents the input reference sequence
   # the second tc Represents the prefix of the output index file
   # Generate six .bt2 A new file
   table The file holds every contig The length of , You can use samtools obtain

samtools faidx Tden.fasta
awk '{print $1 "\t" $2 }' Tden.fasta.fai > Tden.sizes

6. Modify the configuration file config-hicpro.txt

  1-12 Lines do not need to be modified .

  13-25 That's ok ：
  16 That's ok CPU number ,21 Row memory size , The bigger, the faster , The remaining lines need not be changed .

  26-32 That's ok ：
   The last prefix of the original offline data should be _R1/_R2 ending , Of course, it can also be modified in the configuration file to be the same as raw_data The last of the prefixes .

  37-42 That's ok ：
  39 The row is changed to the absolute path to build the index ,40、41 Don't have to change .

  43-49 That's ok ：
  47 The row is the prefix of the index ,48 Line save chromosome /contig The absolute path to the size file .

  64-73 That's ok ：
  67 The line is digested by genomic enzymes bed The absolute path to the file ;
  68 Behavioral cleavage site ,Mobi The cleavage site is GATCGATC;
  69 Minimum fragment length after enzyme digestion ,70 The maximum fragment length after enzyme digestion , The larger the range ,reads More ;
  71,72 The size of the row insert fragment ,HiC The length of the inserted fragment for building the database is generally 300-500bp.

  85-91 That's ok ：
  89 Yes bin The length of , I chose 10kb-1Mb Between ,bin The smaller the value of , The higher the resolution , The more memory space is used for processing , If the data volume of the following diagrams can be reached , The result will be more accurate .
  90 Rows are the form of generating matrices , The optional parameter is ：complete、asis、upper and lower, The default value is upper. If you have to do it later A/B compartment Analytical words , It needs to be changed to complete, Otherwise it will affect PCA The result of the analysis .

3、 ... and 、 function

HiC-Pro -i  Enter the file path  -o  Output file path / file name  -c  The configuration file 

PS： The input file should be in the secondary directory , Cannot be in the current directory or the first level directory .
PPS： The directory where the result files are stored does not need to be built in advance .

Four 、 It's common to report mistakes

1. Local comparison error
   Pairing of R1 and R2 tags …
   Logs: logs/fastq/mergeSAM.log
   make: *** [/home/yaotianyi/biosoft/HIC-PRO/bin/…/scripts//Makefile:144: bowtie_pairing] Error 1
   terms of settlement ： Re index , Run again .
2. Correct errors , Don't get .matrix file
   Run ICE Normalization …
   Logs: logs/sample1/ice_20000.log
   /home/biocon/yaotianyi/biosoft/HIC-PRO/bin/…/scripts//Makefile:191: recipe for target ‘ice_norm’ failed
   make: *** [ice_norm] Error 1
   The problem : Compile and install HiC-Pro Of ice The file uses the environment set by the author , Change to your own installed environment .
   

cd $HiC-Pro insrall PATH$/scripts/
vi ./ice
 Change one line to your own environment ,, Just run it again