Awesome
Installing dicey
Dicey is available as a Bioconda package, as a pre-compiled statically linked binary from Dicey's github release page, as a singularity container SIF file or as a minimal Docker container.
apt-get install -y build-essential g++ cmake zlib1g-dev libbz2-dev liblzma-dev libboost-all-dev autoconf
git clone --recursive https://github.com/gear-genomics/dicey.git
cd dicey/
make all
make install
This will generate the binary bin/dicey
.
Running Dicey
dicey -h
Sequence search in an indexed reference genome
Searching a large reference genome requires a pre-built index on a bgzip compressed genome.
dicey index -o hg19.fa.fm9 hg19.fa.gz
samtools faidx hg19.fa.gz
The indexing step is only required once. You can then search nucleotide sequences at a user-defined edit or hamming distance.
dicey hunt -g hg19.fa.gz TCTCTGCACACACGTTGT | python scripts/json2txt.py
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.
In-silico PCR for a set of primers
Dicey can search for multiple primer pairs, show off-target products and determine PCR amplicons.
echo -e ">FGA_f\nGCCCCATAGGTTTTGAACTCA\n>FGA_r\nTGATTTGTCTGTAATTGCCAGC" > primers.fa
dicey search -c 45 -g hg19.fa.gz primers.fa | python scripts/json2txt.py
The default output is a JSON file that can also be stored in a file.
dicey search -c 45 -o out.json.gz -g hg19.fa.gz primers.fa
Padlock probe design
Dicey can design padlock probes for imaging mRNA in single cells. You need to download an indexed reference genome 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
With these files, you can then design padlock probes for a given gene using
dicey padlock -g Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz -t Homo_sapiens.GRCh38.107.gtf.gz -b data/bar.fa.gz ENSG00000136997
Graphical user interface
You can search primers interactively using our web application silica.
FAQ
-
Dicey cannot find the primer3 config directory
The primer3 config directory is included in the repository. Just clone the repositorygit clone --recursive https://github.com/gear-genomics/dicey.git
and then use the cloned config directorydicey search -i dicey/src/primer3_config/ -g hg19.fa.gz primers.fa
. -
The script
json2txt.py
is not found
Thejson2txt.py
python script is included in the repository. Just clone the repositorygit clone --recursive https://github.com/gear-genomics/dicey.git
and then you will find the script in the./scripts/
subdirectory.
Citation
Dicey is part of the GEAR genomics framework which is described in the below publication.
Rausch, T., Fritz, M.H., Untergasser, A. and Benes, V.
Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.
BMC Genomics 21, 230 (2020).
https://doi.org/10.1186/s12864-020-6635-8
License
Dicey is distributed under the GPL license. Consult the accompanying LICENSE file for more details.