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aaronkw committed Nov 19, 2019
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Expand Up @@ -16,7 +16,7 @@ Jian Zhou, Olga G. Troyanskaya. **Predicting the Effects of Noncoding Variants w
Input
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DeepSEA predicts genomic variant effects on a wide range of chromatin features at the variant position (Transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple hunman cell types). DeepSEA can also be ultilized for predicting chromatin features for any DNA sequence.
DeepSEA predicts genomic variant effects on a wide range of chromatin features at the variant position (Transcription factors binding, DNase I hypersensitive sites, and histone marks in multiple human cell types). DeepSEA can also be ultilized for predicting chromatin features for any DNA sequence.

We support three types of input: vcf, fasta, bed. If you want to predict effects of noncoding variants, use vcf format input. If you want to predict chromatin feature probabilities for DNA sequences, use fasta format. If you want to specify sequences from the human reference genome (GRCh37/hg19), you can use bed format. See below for a quick introduction, and we provide detailed description of format requirement on the DeepSEA input page:

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