Takes as input transcript ids (ENST00000456328.2) and will result in a folder that contains a fasta file with the resulting filtered probes and probe stats including all the created probes with their values, in a table csv format.
The filtering requirements can be changed here aswell to achieve the desired probes. A Final_Probe_results.csv will give information about total created and filtered probes incuding how many probes per transcript are remaining.
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Create conda environement using the provided yml file ->
conda env create -f prodesign_nextflow.yml -
Download reference transcripts
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.transcripts.fa.gzand add them to the Inputs folder. -
unzip the reference file in the inputs folder
gunzip gencode.v37.transcripts.fa.gz. -
Download the latest reference genome with accompanying GTF file in a folder :
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mkdir genome_index -
cd genome_index -
wget http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz -
wget http://ftp.ensembl.org/pub/release-107/gtf/homo_sapiens/Homo_sapiens.GRCh38.107.gtf.gz -
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz -
gunzip Homo_sapiens.GRCh38.107.gtf.gz -
Generate latest reference genome index using STAR.
STAR --runThreadN 40 --runMode genomeGenerate --genomeDir Genome_Dir_GRCH38 --genomeFastaFiles genome_index/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile genome_index/Homo_sapiens.GRCh38.107.gtf -
In probedesign_processes.nf edit the params to match the location of the transcript files,genome index and specify an output folder.
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To run the pipeline activate the conda environment and run: nextflow run probedesign_processes.nf