Patrick Roelli

Would you be able to send me a sample of your data so that I can run it and have a look?

I asked for access

``` results/unmapped.csv tag,count AAGCAGTGGTATCAA,38893 GGGGGGGGGGGGGGG,20759 CCGTACCTCAAAAAA,17644 GCAGTGGTATCAACG,10879 TTCCTGCCAAAAAAA,5855 GTGGTATCAACGCAG,5442 AGCAGTGGTATCAAC,4087 CCGTACCCCAAAAAA,3959 CAGTGGTATCAACGC,3894 ``` It seems pretty reasonable from what I see in the first sample. The unmapped.csv gives you the...

Hello @jhjlee, here are a few answers to your questions 1) I would recommend using about 20% more cells than expected. So for 5k I would use about 6 or...

Hello @jhasselmann808, Yes, each supplementary code used will increase memory usage. The next release does help for the mapping stage and the bottleneck for memory is now more on the...

@jhasselmann808 sounds good :) Btw, are you rinning 1.4.4?

I'm currently working on [a new branch](https://github.com/Hoohm/CITE-seq-Count/tree/feature/namedtuples) that allows deciding on chunk size for the mapping stage and implements parallelization for UMI correction. @heathergeiger I actually don't need all the...

Looking at your log files, this looks more like a problem when the child processes are sending the results back to the main process but never arrive or take too...

Hello @heathergeiger the latest develop branch should offer a big improvement in performance. Can you please try it out?

Yeah sorry, difficult times right now. I'm going to start testing on large datasets as well. I really want this to be possible because I want to allow users to...