diff --git a/README.md b/README.md index 87637fb..efc907a 100644 --- a/README.md +++ b/README.md @@ -23,10 +23,15 @@ Alternatively, you can install dependencies and [install the adVNTR from source] 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. + - 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 [Add Custom VNTR](http://advntr.readthedocs.io/en/latest/tutorial.html#add-custom-vntr-label) for more information. +Alternatively, you can add model for custom VNTR. See [Add Custom VNTR](http://advntr.readthedocs.io/en/latest/tutorial.html#add-custom-vntr-label) for more information about training models for custom VNTRs. Execution: ---------- @@ -34,9 +39,12 @@ Use following command to see the help for running the tool. advntr --help -The program outputs the RU count genotypes of VNTRs. To specify a single VNTR by its ID use ``--vntr_id `` option. +The program outputs the RU count genotypes of trained VNTRs. To specify a single VNTR by its ID use ``--vntr_id `` option. 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. +See the demo below or [Quickstart](http://advntr.readthedocs.io/en/latest/quickstart.html) page to see an example +data set with step-by-step genotyping commands. + Demo input in BAM format ------------------------ * ``--alignment_file`` specifies the alignment file containing mapped and unmapped reads: