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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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===================
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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
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* Python (>2.7) with *pysam (>=0.8.3)*, *bx-python(>=0.5.0)*, *numpy(>=1.8.2)*, and *scipy(>=0.15.1)* libraries
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* R with the *RColorBrewer* and *ggplot2* packages
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* g++ compiler
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* Samtools (>1.0)
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* Unix sort (which support -V option) is required ! For Mac OS user, please install the GNU core utilities !
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1. The `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_ mapper
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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
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3. R with the *RColorBrewer* and *ggplot2 (>2.2.1)* packages
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4. g++ compiler
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5. Samtools (>1.1)
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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
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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.
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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.
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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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@@ -108,7 +110,7 @@ Please be sure that the chromosome names are the same than the ones used in your
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chr1 38791 39255 HIC_chr1_10 0 +
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(...)
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2. **A table file** of chromosomes' size.
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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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@@ -124,20 +126,20 @@ Please be sure that the chromosome names are the same than the ones used in your
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chr10 135534747
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(...)
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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.
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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.
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
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2. Put all input files in a rawdata folder. The input files have to be organized with a folder per sample.
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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
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12. Put all input files in a rawdata folder. The input files have to be organized with one folder per sample, with ;
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