I ran ViralFusionSeq, first on test dataset, given with the software package. I took one the contig assembly sequence generated by tool in the final contig output file. The contig sequence showed BLAST hits with human and hbv virus. I repeated the same procedure with HIV and human, on sample where I manually found clipped sequences that are shared between the two genomes. I then BLAST aligned contig sequences to both human and HIV virus. They only map to HIV. Why am I seeing this? The run was fine without any error reported. The data was DNASeq so I didn't provide any ORF, because I wanted to see all HIV-human integration regions, not only at specific ORF regions.
viral.fusion.pl --config vfs.conf --thread 8 sample_name sample_trim_1.fq sample_trim2.fq
Has anyone noticed such output?
viral.fusion.pl --config vfs.conf --thread 8 sample_name sample_trim_1.fq sample_trim2.fq
Has anyone noticed such output?