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pgRNAFinder: Database
     Genome:
Single

(Unfinished)


Gene name:

1). Data source
The position of protein-coding gene and lncRNA was from Gencode (gencode.v19.annotation.gtf).
The position for enhancer was from FANTOM5 (human_permissive_enhancers_phase_1_and_2.bed, hg19).
2). Design strategy:
Locating in the whole gene or enhancer region.
3). Parameters for designing sgRNA
python run.py -i FAN_enh.hg19 -o FAN_enh.out -g hg19 -f genomic_region -pam NGG -ul 20 -dl 7 -enzys no -s 0.5 -mis 2 -gRNA sg -ontarget all -ota 10 -ote 5 -cg 0.2~0.8 -otsite yes

Pair



Gene name:

1). Data source
The position of protein-coding gene and lncRNA was from Gencode (gencode.v19.annotation.gtf).
The position for additional lncRNAs came from MiTranscriptome.
2). Design strategy:
Locating in the -2kb to 1kb region around TSS (transcription start site). Furthermore, one sgRNA of pgRNA locates in the upstream of TSS and the other one locates in the downstream of TSS.
3). Parameters for designing pgRNA
python run.py -i GEN_code.hg19 -o GEN_code.out -g hg19 -f genomic_region -pam NGG -ul 20 -dl 7 -enzys no -s 0.5 -mis 2 -gRNA pg -ontarget all -ota 10 -ote 5 -cg 0.2~0.8 -dis 0~3000 -cover 0.0~1.0 -strand all -otsite yes

     Other genomes comming soon.