Merge pull request #3 from dovetail-genomics/rtd-hichip-compare

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dovetail-genomics · Apr 19, 2022 · 91c8184 · 91c8184
2 parents cb6872b + 4b5510b
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diff --git a/docs/source/data_sets.rst b/docs/source/data_sets.rst
@@ -3,7 +3,6 @@
 HiChIP Data Sets
 ================
 
-
 To download one of the data sets, simply use the wget command:
 
 .. code-block:: console
@@ -42,3 +41,32 @@ Human, hg38, Peak files from ENCODE project
    :header-rows: 1
    :widths: 12 12 12 40 24
    :class: tight-table
+
+Data used for HiChIP Comparative Analysis (Mouse, mm10)
+-------------------------------------------------------
+
+.. _HCPD:
+
+To get a list of all the files generated from the HiChIP Comparative Analysis tutorial, including the required reference genomes, you can use the command:
+
+.. code-block:: console
+
+   aws s3 ls s3://dovetail.pub/HiChIP/compare_samples/
+ 
+Use wget to download any given file, replacing "s3://" with "https://s3.amazonaws.com/", followed by the remaining path to the file. For example:
+
+.. code-block:: console
+
+   wget https://s3.amazonaws.com/dovetail.pub/HiChIP/compare_samples/Reference_Genome/mm10.fa
+
++------------------+------------------------------------------------------------------------------------------------+
+| Data Set         | Link                                                                                           |
++==================+================================================================================================+
+| Fastqs           | - https://s3.amazonaws.com/dovetail.pub/HiChIP/compare_samples/fastq_inputs/sampleA_R1.fastq.gz|
+| (Sample A)       | - https://s3.amazonaws.com/dovetail.pub/HiChIP/compare_samples/fastq_inputs/sampleA_R2.fastq.gz|
++------------------+------------------------------------------------------------------------------------------------+
+| Fastqs           | - https://s3.amazonaws.com/dovetail.pub/HiChIP/compare_samples/fastq_inputs/sampleB_R1.fastq.gz|
+| (Sample B)       | - https://s3.amazonaws.com/dovetail.pub/HiChIP/compare_samples/fastq_inputs/sampleB_R2.fastq.gz|
++------------------+------------------------------------------------------------------------------------------------+
+
+Note: The full dataset, including input files and generated output is ~183Gb (roughly 5h with a network speed of 10Mb/s). 
diff --git a/docs/source/hichip_compare.rst b/docs/source/hichip_compare.rst
diff --git a/docs/source/images/Fig1_Overview.png b/docs/source/images/Fig1_Overview.png
diff --git a/docs/source/images/Fig2_QC.png b/docs/source/images/Fig2_QC.png
diff --git a/docs/source/images/Fig3_Differential_Looping.png b/docs/source/images/Fig3_Differential_Looping.png
diff --git a/docs/source/images/Fig4_APAs.png b/docs/source/images/Fig4_APAs.png
diff --git a/docs/source/images/Fig5_GO.png b/docs/source/images/Fig5_GO.png
diff --git a/docs/source/images/Fig6_KEGG_Path.png b/docs/source/images/Fig6_KEGG_Path.png
diff --git a/docs/source/images/Fig7_ROI_track.png b/docs/source/images/Fig7_ROI_track.png
diff --git a/docs/source/images/Table1_QC_stats.png b/docs/source/images/Table1_QC_stats.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -58,6 +58,8 @@ Overview
 
    loops
 
+   hichip_compare
+
    plot_arc
 
    1D_peak