CRAFT is a computational pipeline that predicts circRNA sequence and molecular interactions with miRNAs and RBPs, along with their coding potential. CRAFT provides a comprehensive graphical visualization of the results, links to several knowledge databases, extensive functional enrichment analysis and combination of predictions for different circRNAs. CRAFT is a useful tool to help the user explore the potential regulatory networks involving the circRNAs of interest and generate hypotheses about the cooperation of circRNAs into the regulation of biological processes.
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Im now unable to run CRAFT using your test data now earlier it was running fine with these following contents #9
Im a root user, in which i have a directory called test, inside which i have another directory called input. T he contents of the directories are as follows:
1.) root
1.A.) test/ :
a) list_backsplice.txt : 4:143543509-143543972 +
11:33286413-33287511 +
15:64499292-64500166 +
b) params.txt : MO
hsa
Im a root user, in which i have a directory called test, inside which i have another directory called input. T he contents of the directories are as follows:
1.) root 1.A.) test/ : a) list_backsplice.txt : 4:143543509-143543972 + 11:33286413-33287511 + 15:64499292-64500166 + b) params.txt : MO hsa
hg38
score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10 score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10, voteFrac_RBP=0.3.
c) path_files.txt : /data/input/HG38.gtf /data/input/Homo_sapiens.GRCh38.dna.primary_assembly.fa
1.B) input/ :
a) AGO2_binding_sites.bed
b) backsplice_gene_name.txt
c) hg38.02.idx d) hg38.nin e) hg38.nto f) HG38.gtf g) bigWigToWig
h) hg38.fa
i) hg38.not
j)hg38.shd k)Homo_sapiens.GRCh38.104.gtf
l) hg38.00.idx
m) hg38.ndb
n) hg38.nsq o) Homo_sapiens.GRCh38.dna.primary_assembly.fa p) hg38.01.idx
q) hg38.nhr
r) hg38.ntf