Patrick Roelli

The best plot to help would be the yield plot, but for some reason it crashed. What about the star multiqc report? On Fri, 3 Apr 2020, 20:27 Richard Corbett,...

When you say 3000 reads, to mean that's the total for each cell? 3000 reads or umi? On Fri, 3 Apr 2020, 23:10 Richard Corbett, wrote: > Star results... >...

From the cleanqc I see that around 800'000 of your R1 has been trimmed, that means your left with around 200'000 reads after trimming. From there, you loose around 20%...

Yes, seems to be inline with my interpretation.

Hey @YOU-k Our filters are based on either a provided whitelist or on the number of cells provided in the sample.csv file. We don't perform any selection based on expression...

Hello @Hofphi you have nto changed anything and you get a new error? You can't try and run the temporary R script file because it's getting deleted by snakemake on...

I'll take a look into it this week. I'll keep you posted :)

Are your R1 and R2 files having the exact same sample name? It should be like `sample1_R1.fastq.gz`, `sample1_R2.fastq.gz` the prefix has to be exactly the same, in this example: `sample1_`

Could you run the pipeline with the `-p` flag? It will print out the command it tries to execute and we can have a closer look at what's not working.

Yea I was suspecting this would fix it. I was hoping to change multiqc version for a long time but I always had some conflicts coming up and that's why...