@@ -15,7 +15,7 @@ and processes data using the following steps:
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@@ -15,7 +15,7 @@ and processes data using the following steps:
*[Valid pairs detection](#valid-pairs-detection)
*[Valid pairs detection](#valid-pairs-detection)
*[Duplicates removal](#duplicates-removal)
*[Duplicates removal](#duplicates-removal)
*[Contact maps](#hicpro-contact-maps)
*[Contact maps](#hicpro-contact-maps)
*[Contact maps](#contact-maps)
*[Hi-C contact maps](#hic-contact-maps)
*[Downstream analysis](#downstream-analysis)
*[Downstream analysis](#downstream-analysis)
*[Distance decay](#distance-decay)
*[Distance decay](#distance-decay)
*[Compartments calling](#compartments calling)
*[Compartments calling](#compartments calling)
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@@ -193,7 +193,7 @@ files.
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@@ -193,7 +193,7 @@ files.
This format is memory efficient, and is compatible with several software for
This format is memory efficient, and is compatible with several software for
downstream analysis.
downstream analysis.
## Contact maps
## Hi-C contact maps
Contact maps are usually stored as simple txt (`HiC-Pro`), .hic (`Juicer/Juicebox`) and .(m)cool (`cooler/Higlass`) formats.
Contact maps are usually stored as simple txt (`HiC-Pro`), .hic (`Juicer/Juicebox`) and .(m)cool (`cooler/Higlass`) formats.
Note that .cool and .hic format are compressed and usually much more efficient that the txt format.
Note that .cool and .hic format are compressed and usually much more efficient that the txt format.
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@@ -227,6 +227,7 @@ Although different methods have been proposed for compartment calling, the stand
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@@ -227,6 +227,7 @@ Although different methods have been proposed for compartment calling, the stand
Here, we use the implementation available in the [`cooltools`](https://cooltools.readthedocs.io/en/lates) package.
Here, we use the implementation available in the [`cooltools`](https://cooltools.readthedocs.io/en/lates) package.
Results are available in **`results/compartments/`** folder and includes :
Results are available in **`results/compartments/`** folder and includes :
*`*cis.vecs.tsv`: eigenvectors decomposition along the genome
*`*cis.vecs.tsv`: eigenvectors decomposition along the genome
*`*cis.lam.txt`: eigenvalues associated with the eigenvectors
*`*cis.lam.txt`: eigenvalues associated with the eigenvectors
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@@ -236,9 +237,11 @@ TADs has been described as functional units of the genome.
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@@ -236,9 +237,11 @@ TADs has been described as functional units of the genome.
While contacts between genes and regulatority elements can occur within a single TADs, contacts between TADs are much less frequent, mainly due to the presence of insulation protein (such as CTCF) at their boundaries. Looking at Hi-C maps, TADs look like triangles around the diagonal. According to the contact map resolutions, TADs appear as hierarchical structures with a median size around 1Mb (in mammals), as well as smaller structures usually called sub-TADs of smaller size.
While contacts between genes and regulatority elements can occur within a single TADs, contacts between TADs are much less frequent, mainly due to the presence of insulation protein (such as CTCF) at their boundaries. Looking at Hi-C maps, TADs look like triangles around the diagonal. According to the contact map resolutions, TADs appear as hierarchical structures with a median size around 1Mb (in mammals), as well as smaller structures usually called sub-TADs of smaller size.
TADs calling remains a challenging task, and even if many methods have been proposed in the last decade, little overlap have been found between their results.
TADs calling remains a challenging task, and even if many methods have been proposed in the last decade, little overlap have been found between their results.
Currently, the pipeline proposes two approaches :
Currently, the pipeline proposes two approaches :
- Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
-[`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
* Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
*[`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
Usually, TADs results are presented as simple BED files, or bigWig files, with the position of boundaries along the genome.
Usually, TADs results are presented as simple BED files, or bigWig files, with the position of boundaries along the genome.
