About CIRCprimerXL

How to cite

https://www.frontiersin.org/articles/10.3389/fbinf.2022.834655/full

Vromman M, Anckaert J, Vandesompele J and Volders P-J (2022) CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification. Front. Bioinform. 2:834655. doi: 10.3389/fbinf.2022.834655

General information

The CIRCprimerXL pipeline scripts are primarily written in Python (version 3.8.10). The pipeline is written using Nextflow (version 20.10.0.5430) and runs in a Docker container (version 20.10.11). The backend of the web application is built with Python (version 3.8-slim-buster) and the Flask framework (version 2.0.2), while the frontend is based on Bootstrap (version 5.1.).

Used genomes

human	DNA	http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
	cDNA	http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
	ncRNA	http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz
	SNPs	http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp153Common.bb
	exon annotation	http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz
	canonical transcripts	https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/MANE.GRCh38.v0.95.select_ensembl_genomic.gtf.gz
Xenopus tropicalis	DNA	http://ftp.ensembl.org/pub/release-104/fasta/xenopus_tropicalis/dna/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.dna.toplevel.fa.gz
	cDNA	http://ftp.ensembl.org/pub/release-104/fasta/xenopus_tropicalis/cdna/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.cdna.all.fa.gz
	ncRNA	http://ftp.ensembl.org/pub/release-104/fasta/xenopus_tropicalis/ncrna/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.ncrna.fa.gz
	exon annotation	http://ftp.ensembl.org/pub/release-104/gtf/xenopus_tropicalis/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.104.gtf.gz
mouse	DNA	http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
	cDNA	http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz
	ncRNA	http://ftp.ensembl.org/pub/release-104/fasta/mus_musculus/ncrna/Mus_musculus.GRCm39.ncrna.fa.gz
	exon annotation	http://ftp.ensembl.org/pub/release-104/gtf/mus_musculus/Mus_musculus.GRCm39.104.gtf.gz
C. elegans	DNA	http://ftp.ensembl.org/pub/release-104/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz
	cDNA	http://ftp.ensembl.org/pub/release-104/fasta/caenorhabditis_elegans/cdna/Caenorhabditis_elegans.WBcel235.cdna.all.fa.gz
	ncRNA	http://ftp.ensembl.org/pub/release-104/fasta/caenorhabditis_elegans/ncrna/Caenorhabditis_elegans.WBcel235.ncrna.fa.gz
	exon annotation	http://ftp.ensembl.org/pub/release-104/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.104.gtf.gz
zebrafish	DNA	http://ftp.ensembl.org/pub/release-104/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz
	cDNA	http://ftp.ensembl.org/pub/release-104/fasta/danio_rerio/cdna/Danio_rerio.GRCz11.cdna.all.fa.gz
	ncRNA	http://ftp.ensembl.org/pub/release-104/fasta/danio_rerio/ncrna/Danio_rerio.GRCz11.ncrna.fa.gz
	exon annotation	http://ftp.ensembl.org/pub/release-104/gtf/danio_rerio/Danio_rerio.GRCz11.104.gtf.gz
rat	DNA	http://ftp.ensembl.org/pub/release-104/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
	cDNA	http://ftp.ensembl.org/pub/release-104/fasta/rattus_norvegicus/cdna/Rattus_norvegicus.Rnor_6.0.cdna.all.fa.gz
	ncRNA	http://ftp.ensembl.org/pub/release-104/fasta/rattus_norvegicus/ncrna/Rattus_norvegicus.Rnor_6.0.ncrna.fa.gz
	exon annotation	http://ftp.ensembl.org/pub/release-104/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.104.gtf.gz