Probedesign

Work in progress

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.

• 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.gz and 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 :

• 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.

• To run the pipeline activate the conda environment and run: nextflow run probedesign_processes.nf