diff --git a/docs/installation.rst b/docs/installation.rst index 16c78a9..5f7fc16 100644 --- 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 `_ 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 `_ 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 `_ 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 index 7f59936..99a7494 100644 --- 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 `_ 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 `_ 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 `_ in wiki. Then, download `simulated sequencing data of a human sample `_. @@ -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 `_, you need the organism (here, human) reference -genome to train a model for a specific VNTR. +`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 `_ 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.