Viktor Petukhov

Thanks a lot for the note! I'll fix it.

In general, reads can be aligned on one of two strands. And a gtf file contains genes with information about strands. And you want to split it by the alignment...

@jggatter , it shouldn't be that hard to add: add new flag to the `dropest` CLI, new field to the resulting rds file and some `if`s to the bam parsing...

> I'd be interested in taking a look but currently I have several other priorities for my project! I may or may not reach out to you in the distant...

> So if I understood the above conversation correctly, the current best way is to split the bam file and run twice dropEst with the transcriptome annotation also split into...

> Would it be feasible to support output of a deduplicated BAM as well? Unfortunately, it doesn't fit the workflow. Merging duplicated UMIs requires a lot of R calls, but...

> Issue fixed by modifying two parameters: +1 > > drop_seq.xml: unlimited > re-run dropest without -u Interesting, thanks for the explanation! I'll take a look on what can be...

> As I've learned from here, this package was not properly tested with drop-seq dataset. It works somehow smoothly with my drop-seq data. Again, thanks for the note! > The...

Hi @k3yavi , Ohm, this function should work really fast. Can you please give me values of `max_umi_per_gene` and `length(umi_probabilities)`?

4 millions UMIs per gene? It's definitely not a correct number. Can you please publish your dropEst log?