I have some overrepresented reads in my RNA-Seq for Salmonella
1. ssrA
2. genomic DNA
3. short reads (<20 bp), they are not adapter sequence and were not found in Salmonella genome by blast
What should I to the sequence
1. I do not care expression of ssrA. Should I leave them or remove them ?
2. For overrepresented genomic DNA. Removing will result in losing real peaks. Should I just leave it?
3. The short reads do not have hits on genomic. Should I just leave them or remove them?
1. ssrA
2. genomic DNA
3. short reads (<20 bp), they are not adapter sequence and were not found in Salmonella genome by blast
What should I to the sequence
1. I do not care expression of ssrA. Should I leave them or remove them ?
2. For overrepresented genomic DNA. Removing will result in losing real peaks. Should I just leave it?
3. The short reads do not have hits on genomic. Should I just leave them or remove them?