Shian Su

No, I don't believe we ever properly addressed this. Thanks for bringing it to my attention again, I might have some Christmas coding to do.

Agreed, there's already a hidden function in the works [here](https://github.com/LuyiTian/scPipe/blob/master/R/get_read_str.R). Once I write some documentation and add more protocols I will make it a public function.

Just realised it's not so hidden as I apparently decided to export it 2 months ago! But yes, it currently supports only 4 protocols, would love to add more.

Hello Izzy, Thanks for your issue report. The example isn't meant to produce a table full of 0s. It's unclear what kind of bug is causing this and I am...

Sorry @IzzyJRussell for the delayed response, I've been travelling for the past couple of weeks. I've narrowed the issue down to the fact that `sc_demultiplex(file.path(data_dir, "out.map.bam"), data_dir, barcode_annotation_fn,has_UMI=FALSE)` has `has_UMI=FALSE`...

I have only converted from raw BCL once myself, perhaps @LuyiTian can look into this. As far as I know this can be done by wrapping around bcl2fastq, the difficult...

Also having a similar issue ``` > read_tsv("/var/folders/3p/qh68nr3j5h3054n7llf_9l1r00025j/T/RtmphWTjFR/B6Cast_Prom_1_bl6.tsv") Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value ``` ``` $ head /var/folders/3p/qh68nr3j5h3054n7llf_9l1r00025j/T/RtmpQIfXAu/B6Cast_Prom_1_bl6.txt chr pos total...

I think I understand that "position sorted" is the same as "sequence name and then by leftmost coordinate", as the sequence is considered a part of the entry's position. Still,...

This would be very useful for me, I run Dorado on a HPC environment and it'd be very useful to know how it's progressing.

I consider the amount of throughput of a long-read experiment to be the gigabases sequenced rather than number of reads. By extension I think of the proportion of gigabases aligned...