Hi,
I was wondering whether for the counting part there is a possibility to use SE BC fastq (read1) and supply a UMI fastq (read2)?
In addition, a few things are unclear to me regarding the workflow:
1) is UMI collapsing happening per BC-UMI or across BCs per UMI? If the same UMI is associated with multiple BCs, how is this being handled?
2) Does it require a perfect match between the association file BC sequences and the ones observed in read1 fastq?
3) Related to 2), are the base qualities somehow taken into account?
Hi, I was wondering whether for the counting part there is a possibility to use SE BC fastq (read1) and supply a UMI fastq (read2)? In addition, a few things are unclear to me regarding the workflow: 1) is UMI collapsing happening per BC-UMI or across BCs per UMI? If the same UMI is associated with multiple BCs, how is this being handled? 2) Does it require a perfect match between the association file BC sequences and the ones observed in read1 fastq? 3) Related to 2), are the base qualities somehow taken into account?
Thank you a lot!