Patrick Roelli

Hello @naila53 this comes from the fact that the cells have two barcodes. One for RNA and one for Protein data. Version 1.5.0 will deal with this on the fly...

Yes, it's been a thorn in my side for a while now. I've worked on 1.5.0 today: https://github.com/Hoohm/CITE-seq-Count/tree/feature/cells_argument I'm nearly done with automated translation on the fly by just selecting...

Hello @cpflueger2016 Maybe I should write a bit more details about that part. UMI counts are "demultiplexed" reads. Meaning that you get one count per combination of cell + UMI...

Hey @cpflueger2016 sorry for the late response. It is a bit strange that you have some tags in some cells that are more amplified. I'm noticing this on tag_6 for...

I guess there is something in the protocol that behaves differently than expected. I haven't seen something like it yet no, sorry. Would you be able to describe the protocol...

Yes there is a `--debug` flag which will show you each match result and the proposed match. This is not kmer based, it's a simple fuzzy grep so I'm confident...

That's some nice digging you did there :) There is no way to do what you need with CITE-seq-Count especially since the dict that collects counts is based on the...

Hey @cpflueger2016 had a few minutes to spend on this. the [switch_branch](https://github.com/Hoohm/CITE-seq-Count/tree/switch_mod) now works as we discussed. Whenever there is more than one most_common, It prints out the top 10...

Have you updated the code? https://github.com/KirstieJane/STEMMRoleModels/wiki/Syncing-your-fork-to-the-original-repository-via-the-browser

This is strange. Can you double check that you call it like : `CITE-seq-Count -R1 R1.fastq.gz -R2 R2.fastq.gz --tags tags.csv -cbf 1 -cbl 16 -umif 17 -umil 28 -cells 10...