Daniel Liu

When you pass in the `--paired` flag, any read1 that is removed will cause its corresponding read2 to be removed too. (Same behavior as UMI-tools)

Sorry for the delay, there is a v1.0.0 release now.

For tracking clusters with `--tag`, two passes need to be made over the input. Therefore, this is only possible with an input file. The reason why UMICollapse is designed this...

Hm, that is definitely weird. I don't know what's wrong off the top of my head. What command did you run for UMICollapse? Does this happen for other bam records?

For the fastq mode, reads are compared by both the read sequence and the UMI. So two reads will only be grouped together and collapsed if they have the same...

Not at the moment. You can work around this by filtering out unmapped reads from your file before deduplication with `samtools` like [here](https://www.biostars.org/p/56246/).

Hey, this is a good suggestion. For now, a potential workaround is to write a simple script that extracts the `RX` tag and puts it at the end of the...

For both the average and the max statistics, they are calculated using the number of unique UMIs at each alignment position. The number of unique UMIs is counted by identity...

Deduplicating typically means the whole process. There's two steps: 1. find unique UMIs 2. group the unique UMIs in an error-tolerant way. Collapsing is used sometimes because only one UMI...

Ah thank you so much! (I have not published packages to bioconda before.)