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Old 07-06-2018, 11:21 AM   #1
Location: Pittsburgh, PA

Join Date: May 2010
Posts: 22
Default ViralFusionSeq not finding human-virus fusion regions

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. --config vfs.conf --thread 8 sample_name sample_trim_1.fq sample_trim2.fq

Has anyone noticed such output?
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