update readthedocs documentations

mehrdadbakhtiari · Mar 24, 2019 · e1f0dde · e1f0dde
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diff --git a/docs/installation.rst b/docs/installation.rst
@@ -23,9 +23,11 @@ adVNTR could be invoked from command line with ``advntr``
 
 Data Requirements
 -----------------
+In order to genotype VNTRs, you need to either train models for loci of interest or use pre-trained models (recommended):
 * To run adVNTR on trained VNTR models:
-    - Download `vntr_data.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data.zip>`_ and extract it inside the project directory.
-Alternatively, you can add model for custom VNTR. See :ref:`add-custom-vntr-label` for more information.
+    - Download `vntr_data_recommended_loci.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data_recommended_loci.zip>`_ and extract it inside the project directory. This includes a set of pre-trained VNTR models for Illumina (6719 loci) and Pacbio (8960 loci) sequencing data.
+    - You can also download and use `vntr_data_genic_loci.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data_genic_loci.zip>`_ for 158522 VNTRs that results in having much longer running time.
+Alternatively, you can add model for custom VNTR. See :ref:`add-custom-vntr-label` for more information about training models for custom VNTRs.
 
 Execution:
 ----------

diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -21,9 +21,9 @@ To install adVNTR, run these commands:
 Genotype Predefined VNTR in Simulated Data
 ------------------------------------------
 To genotype a VNTR in the simulated dataset, one option is to use predefined models.
-Download `vntr_data.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data.zip>`_ and extract it inside the
-project directory to use these models from human genome. Here, we genotype a VNTR with id 301645 that corresponds to a
-disease-linked VNTR. The list of some known VNTRs and their ID is available at
+Download `vntr_data_recommended_loci.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data_recommended_loci.zip>`_ and
+extract it inside the project directory to use these models from human genome. Here, we genotype a VNTR with id 301645
+that corresponds to a disease-linked VNTR. The list of some known VNTRs and their ID is available at
 `Disease-linked-VNTRs page <https://github.com/mehrdadbakhtiari/adVNTR/wiki/Disease-linked-VNTRs>`_ in wiki.
 
 Then, download `simulated sequencing data of a human sample <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/quickstart/>`_.
@@ -37,8 +37,8 @@ Run this command to get 2/5 genotype for this VNTR.
 Genotype Custom VNTR
 --------------------
 You can train a new model for a VNTR that doesn't exist in predefined models. Instead of downloading
-`vntr_data.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data.zip>`_, you need the organism (here, human) reference
-genome to train a model for a specific VNTR.
+`vntr_data_recommended_loci.zip <https://cseweb.ucsd.edu/~mbakhtia/adVNTR/vntr_data_recommended_loci.zip>`_, you need
+the organism (here, human) reference genome to train a model for a specific VNTR.
 `Download chromosome 21 of hg19 <http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr21.fa.gz>`_ and extract it.
 It is recommended to have full reference genome of the organism to add the model, however, we use a single chromosome
 in quickstart since it is easier to download and runs faster.