I am trying to analyze RNA-seq (Human) samples for viral integration. Till now I have come up with few steps for analysis:
1) aligning the RNA-seq data to reference human transcriptome (STAR)
2) separating the unmapped reads/discordant reads
3) aligning the unmapped reads to viral sequence (STAR)
I have done the above 4 steps so far. I am not sure how I should proceed. Also, the alignment of unmapped reads and viral sequence gave me only 0.03% of uniquely mapped reads which is around 1000 reads as per the data I provided.
Can someone help me here for proceeding the analysis. ?
Thank you in advance