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Xihao Li authored Dec 9, 2021
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Expand Up @@ -5,11 +5,11 @@ Thank you for your interest in MACIE. MACIE (Multi-dimensional Annotation Class


## Data Availability and Code Reproducibility
The MACIE scores (and other integrative scores) used in all benchmarking examples are available for download [here](https://drive.google.com/drive/folders/1gzqsfgaO1WCh5pAQUgVlUNsX9HYneO7p?usp=sharing). Precomputed MACIE scores for every possible variant in the human genome are available for download via Zenodo: [Part 1 (Chr1 - Chr3)](https://zenodo.org/record/5755656), [Part 2 (Chr4 - Chr7)](https://zenodo.org/record/5756449), [Part 3 (Chr8 - Chr13)](https://zenodo.org/record/5756479), [Part 4 (Chr14 - Chr22)](https://zenodo.org/record/5756563). These are compressed with the bgzip utility, and indexed with tabix, both of which are part of the [Samtools software suite](http:https://www.htslib.org/). In addition, tabix provides a means of efficiently extracting subsets of the data defined by genomic regions. For example, the command line
The MACIE scores (and other integrative scores) used in all benchmarking examples are available for download [here](https://drive.google.com/drive/folders/1gzqsfgaO1WCh5pAQUgVlUNsX9HYneO7p?usp=sharing). Precomputed MACIE scores for every possible variant in the human genome are available for download via Zenodo: [Part 1 (Chr1 - Chr3)](https://zenodo.org/record/5755656), [Part 2 (Chr4 - Chr7)](https://zenodo.org/record/5756449), [Part 3 (Chr8 - Chr13)](https://zenodo.org/record/5756479), [Part 4 (Chr14 - Chr22)](https://zenodo.org/record/5756563). These are compressed with the bgzip utility, and indexed with tabix, both of which are part of the [Samtools software suite](https:https://www.htslib.org). In addition, tabix provides a means of efficiently extracting subsets of the data defined by genomic regions. For example, the command line

`tabix MACIE_hg19_noncoding_chr1.tab.bgz 1:20000-30000 > Subset.txt`

extracts all variants on chromosome 1 from position 20,000 through 30,000 and writes them to the file Subset.txt. In this example, the tabix index file, `MACIE_hg19_noncoding_chr1.tab.bgz.tbi`, needs to be in the same directory as the main data file, `MACIE_hg19_noncoding_chr1.tab.bgz`. Samtools, including bgzip and tabix, is available [here](http:https://www.htslib.org/download).
extracts all variants on chromosome 1 from position 20,000 through 30,000 and writes them to the file Subset.txt. In this example, the tabix index file, `MACIE_hg19_noncoding_chr1.tab.bgz.tbi`, needs to be in the same directory as the main data file, `MACIE_hg19_noncoding_chr1.tab.bgz`. Samtools, including bgzip and tabix, is available [here](https:https://www.htslib.org/download).

The code used for training MACIE models are available [here](https://github.com/xihaoli/MACIE/blob/main/code/MACIE.py).

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