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tobiasrausch committed Aug 3, 2023
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Expand Up @@ -42,7 +42,7 @@ You can also redirect the output in JSON format to a file.

`dicey hunt -g hg19.fa.gz -o out.json.gz TCTCTGCACACACGTTGT`

Pre-built genome indices for commonly used reference genomes are available for [download here](https://gear.embl.de/data/tracy/).
Pre-built genome indices for commonly used reference genomes are available for [download here](https://gear-genomics.embl.de/data/tracy/).


## In-silico PCR for a set of primers
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## Padlock probe design

Dicey can design padlock probes for imaging mRNA in single cells. You need to download an [indexed reference genome](https://gear.embl.de/data/tracy/) and a matching GTF file, e.g., for GRCh38:
Dicey can design padlock probes for imaging mRNA in single cells. You need to download an [indexed reference genome](https://gear-genomics.embl.de/data/tracy/) and a matching GTF file, e.g., for GRCh38:

`wget http://ftp.ensembl.org/pub/release-107/gtf/homo_sapiens/Homo_sapiens.GRCh38.107.gtf.gz`

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