Tobias Neumann

Hi - how exactly did you create the conda environment and which system are you using. MacOS?

Hi @drowsygoat what about if you use a plain ``` conda create --name slam2 slamdunk ``` so not force it to come from the bioconda channel?

Hm does anything speak against using Docker?

@drowsygoat Hm if that is the case, did you make sure you specify the proper resources during docker run? Like `--cpus 2 -m 8g `. Also, did you check your...

Hi @penguinmeow sorry for the slow response. I think you can first try it with paired-end alignments. For this I guess you need to get rid of the `-l` and...

Hi Zhen, sorry for not being clear - the `-l` should only be removed for the `ngm` call - for the actual slamdunk commands you should supply the read-length with...

Hi, 1. Not really, but there is a paper from the same lab dedicated to small RNAs https://pubmed.ncbi.nlm.nih.gov/31350118/ 2. What are you having difficulties with?

Can you go to the map folder and have a look at the log files there - what do they say?

Hm how did you install slamdunk? Via conda? Or Docker? Sounds like NGM was not installed.

Then this is weird, did you set up all channels correctly? What if you redo it like this? ``` conda config --add channels defaults conda config --add channels bioconda conda...