#  Sequencing inDrop Libraries 

 



 **Most users sequence their libraries on a NextSeq 75bp run:**

 Read 1: 61   
Read 2: 14  
Index 1: 8  
Index 2: 8

 It is common to have 70-80% valid reads after filtering for valid cell barcodes.

 **Sequencing on a their libraries on a NovaSeq 100bp run:**

 Read 1: 86   
Read 2: 14  
Index 1: 8  
Index 2: 8

 Our current experience with inDrops runs on a NovaSeq indicate that we are having some trouble on the Index reads. Some libraries are only getting 6 bp of the 8bp index read. This is leading to a lower percent of valid reads after filtering for valid barcodes 50-60%. Due to this, the NovaSeq seems most cost effective if sequencing with the full S1 or S2 flow cells.

 ![library structure](/sites/g/files/omnuum5501/files/singlecellcore/files/seq_indrops.png)