Apart from the obvious factor -- library concentration -- I was wondering what other variables affect cluster density. In other words, if one were to use qPCR for library quantification and load all samples at the same pM concentration, what factors would affect cluster densities? Which factors have the biggest influence i.e. are the biggest source of cluster density variability?
Here are some of my ideas, but I was hoping to draw on the experience here. Please comment and/or add to my list:
1. Cluster station or cbot?
2. Average fragment length of library
3. GC-content of library
4. Type of sample
- gDNA
- Methyl-seq
- mRNA (cDNA)
- small RNA
- GEX
- ChIP-seq
- multiplexed/barcoded
- others?
5. Type of flow-cell (SE or PE)
6. Lot number of flow-cell
7. Type of cluster generation kit
8. Version of cluster generation kit
9. Lot number of cluster generation kit
Anything else?
Here are some of my ideas, but I was hoping to draw on the experience here. Please comment and/or add to my list:
1. Cluster station or cbot?
2. Average fragment length of library
3. GC-content of library
4. Type of sample
- gDNA
- Methyl-seq
- mRNA (cDNA)
- small RNA
- GEX
- ChIP-seq
- multiplexed/barcoded
- others?
5. Type of flow-cell (SE or PE)
6. Lot number of flow-cell
7. Type of cluster generation kit
8. Version of cluster generation kit
9. Lot number of cluster generation kit
Anything else?
Comment