Plant pathogen interaction RNAseq analysis
Hi, Yesterday I post a question about different mapping percentage for control and treated (virus infected) plant. Later I found that about 25% of my reads from treated libraries are mapping with the virus genome I used for infection that leads the discrepancy in mapping rate. My question is hoq to compare the control and treated samples in this case when there is already 25% mapping difference. Will it not affect the final counts for this sample? Greatly appreciate any suggestion!
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