Will mapping Read 1 in Single Cell 3' sequencing increase mapping accuracy or not?

Why lots of pipeline of 3` sequencing (such as zUMI, scruff) do not map Read 1, including barcode and UMI, as PE mode mapping?

Though its low quality bases after varying-length ployT issue, will the Read 1 be helpful for mapping accurency to add this information after trimming barcode+UMI+ployT?

A related discussion about 5` sequencing is here for STAR.

"Cell Ranger has a "PE" mode that gets activated when the barcode read (read 1) is longer than 50 nt - and so it gets used for both cDNA and barcode." as indicated in the issue above.

Thank you.


singlecell


zUMI


mapping


3`sequencing


scruff

• 72 views



Source link