I am currently engaged in an HIV integration site analysis, having already aligned my fastq samples to the cat-human-host reference and obtained the corresponding bam files. However, the specific HIV virus I intend to use carries a GFP marker. Can I incorporate my own virus genome in the provided scripts (such as chimeric.py, orientation.py, etc.) instead of using the K03455 virus genome?
I am currently engaged in an HIV integration site analysis, having already aligned my fastq samples to the cat-human-host reference and obtained the corresponding bam files. However, the specific HIV virus I intend to use carries a GFP marker. Can I incorporate my own virus genome in the provided scripts (such as chimeric.py, orientation.py, etc.) instead of using the K03455 virus genome?
Best, Cam