I had some questions regarding the duplicate removal steps. With the following code, I understand that we are removing duplicates based on identical UMI, tagmentation site, reverse transcription index and ligation adaptor index...
My questions are:
_1. What exactly is the difference between the sam files in rmdup_sam and rmdup_sam_2 folders?
Why are two rounds of the same script being run post barcode attachment?
The previous step is barcode+UMI attachment but the way I read it, we are only attaching the barcode, does that sound right?_ I don't understand where the UMI is being defined. Am I missing something?
I am trying to understand which step is doing exactly what within sci3_main.sh and hence the questions.
Thank you!
Hi Dr. Cao,
I had some questions regarding the duplicate removal steps. With the following code, I understand that we are removing duplicates based on identical UMI, tagmentation site, reverse transcription index and ligation adaptor index...
My questions are: _1. What exactly is the difference between the sam files in rmdup_sam and rmdup_sam_2 folders?
I am trying to understand which step is doing exactly what within sci3_main.sh and hence the questions. Thank you!
Regards, Deep