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| .. Nicolas Servant | ||
| .. HiC-Pro | ||
| .. v2.5.0 | ||
| .. 15-04-02 | ||
| .. v2.10.0 | ||
| .. 17-12-22 | ||
| HiC-Pro Quick Start Guide | ||
| ************************* | ||
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@@ -16,6 +16,10 @@ See LOGBOOK for details about the HiC-Pro developments | |
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| See LICENSE for license information | ||
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| Where to find help ? | ||
| ==================== | ||
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| For any question about HiC-Pro, please contact [email protected] or use the `HiC-Pro forum <https://groups.google.com/forum/#!forum/hic-pro>`_ ! | ||
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| What is HiC-Pro ? | ||
| ================= | ||
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@@ -30,19 +34,17 @@ If you use HiC-Pro, please cite : | |
| HiC-Pro: An optimized and flexible pipeline for Hi-C processing. *Servant N., Varoquaux N., Lajoie BR., Viara E., Chen CJ., Vert JP., Dekker J., Heard E., Barillot E.* Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x | ||
| `http://www.genomebiology.com/2015/16/1/259 <http://www.genomebiology.com/2015/16/1/259>`_ | ||
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| For any question about HiC-Pro, please contact [email protected] or use the `HiC-Pro forum <https://groups.google.com/forum/#!forum/hic-pro>`_ ! | ||
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| How to install it ? | ||
| =================== | ||
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| The HiC-Pro pipeline requires the following dependencies : | ||
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| * The `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_ mapper | ||
| * Python (>2.7) with *pysam (>=0.8.3)*, *bx-python(>=0.5.0)*, *numpy(>=1.8.2)*, and *scipy(>=0.15.1)* libraries | ||
| * R with the *RColorBrewer* and *ggplot2* packages | ||
| * g++ compiler | ||
| * Samtools (>1.0) | ||
| * Unix sort (which support -V option) is required ! For Mac OS user, please install the GNU core utilities ! | ||
| 1. The `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_ mapper | ||
| 2. Python (>2.7, python-3 is not supported) with *pysam (>=0.8.3)*, *bx-python(>=0.5.0)*, *numpy(>=1.8.2)*, and *scipy(>=0.15.1)* libraries | ||
| 3. R with the *RColorBrewer* and *ggplot2 (>2.2.1)* packages | ||
| 4. g++ compiler | ||
| 5. Samtools (>1.1) | ||
| 6. Unix sort (which support -V option) is required ! For Mac OS user, please install the GNU core utilities ! | ||
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| Bowtie >2.2.2 is strongly recommanded for allele specific analysis. | ||
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@@ -92,7 +94,7 @@ Annotation Files | |
| In order to process the raw data, HiC-Pro requires three annotation files. Note that the pipeline is provided with some Human and Mouse annotation files. | ||
| Please be sure that the chromosome names are the same than the ones used in your bowtie indexes ! | ||
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| 1. **A BED file** of the restriction fragments after digestion. This file depends both of the restriction enzyme and the reference genome. See the :ref:`FAQ <FAQ>` and the :ref:`HiC-Pro utilities <UTILS>` for details about how to generate this file. A few annotation files are provided with the HiC-Pro sources. | ||
| 7. **A BED file** of the restriction fragments after digestion. This file depends both of the restriction enzyme and the reference genome. See the :ref:`FAQ <FAQ>` and the :ref:`HiC-Pro utilities <UTILS>` for details about how to generate this file. A few annotation files are provided with the HiC-Pro sources as examples. | ||
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| :: | ||
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| chr1 38791 39255 HIC_chr1_10 0 + | ||
| (...) | ||
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| 2. **A table file** of chromosomes' size. | ||
| 8. **A table file** of chromosomes' size. This file can be easily find on the UCSC genome browser. Of note, pay attention to the contigs or scaffolds, and be aware that HiC-pro will generate a map per chromosome pair. For model organisms such as Human or Mouse, which are well annotated, we usually recommand to remove all scaffolds. | ||
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| :: | ||
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| chr10 135534747 | ||
| (...) | ||
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| 3. **The bowtie2 indexes**. See `the bowtie2 manual page <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_ for details about how to create such indexes. | ||
| 9. **The bowtie2 indexes**. See `the bowtie2 manual page <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_ for details about how to create such indexes. | ||
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| How to use it ? | ||
| =============== | ||
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| 0. First have a look at the help message ! | ||
| 10. First have a look at the help message ! | ||
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| .. code-block:: guess | ||
| HiC-Pro --help | ||
| usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v] | ||
| Use option -h|--help for more information | ||
| HiC-Pro 2.7.0 | ||
| HiC-Pro 2.10.0 | ||
| --------------- | ||
| OPTIONS | ||
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| [-h|--help]: help | ||
| [-v|--version]: version | ||
| 1. Copy and edit the configuration file *'config-hicpro.txt'* in your local folder. See the :ref:`manual <MANUAL>` for details about the configuration file | ||
| 2. Put all input files in a rawdata folder. The input files have to be organized with a folder per sample. | ||
| 11. Copy and edit the configuration file *'config-hicpro.txt'* in your local folder. See the :ref:`manual <MANUAL>` for details about the configuration file | ||
| 12. Put all input files in a rawdata folder. The input files have to be organized with one folder per sample, with ; | ||
| * PATH_TO_MY_DATA | ||
| * + sample1 | ||
| ++ file1_R1.fastq.gz | ||
| ++ file1_R2.fastq.gz | ||
| ++ ... | ||
| * + sample2 | ||
| ++ file1_R1.fastq.gz | ||
| ++ file1_R2.fastq.gz | ||
| *... | ||
| 3. Run HiC-Pro | ||
| * **On your laptop** | ||
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| .. code-block:: guess | ||
| MY_INSTALL_PATH/bin/HiC-Pro -i FULL_PATH_TO_RAW_DATA -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE | ||
| MY_INSTALL_PATH/bin/HiC-Pro -i FULL_PATH_TO_DATA_FOLDER -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE | ||
| * **Using a cluster (TORQUE/SGE/SLURM/LSF)** | ||
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| .. code-block:: guess | ||
| MY_INSTALL_PATH/bin/HiC-Pro -i FULL_PATH_TO_RAW_DATA -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE -p | ||
| MY_INSTALL_PATH/bin/HiC-Pro -i FULL_PATH_TO_DATA_FOLDER -o FULL_PATH_TO_OUTPUTS -c MY_LOCAL_CONFIG_FILE -p | ||
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| user 3m24.493s | ||
| sys 0m33.151s | ||
| Using HiC-Pro in a Singularity container | ||
| ======================================== | ||
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| HiC-Pro v2.10.0 provides a Singularity container to overcome any limitations with the installation process. | ||
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| 1- Install singularity | ||
| http://singularity.lbl.gov/install-linux | ||
| http://singularity.lbl.gov/install-mac | ||
| http://singularity.lbl.gov/install-windows | ||
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| 2- Build the singularity HiC-Pro image | ||
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| >> singularity create -s 5000 hicpro_ubuntu.img | ||
| >> sudo singularity -d bootstrap hicpro_ubuntu.img hicpro_singularity | ||
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| 3- Run HiC-pro | ||
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| >> singularity exec HiC-Pro -h | ||
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