Tobias Neumann

Hm is there maybe a problem with the fastq file? Is there a way you could send it over so I test it on my end? It's tough to pinpoint...

Hi @zhouyjjj - sorry for the long radio silence, I was on holiday. Currently Slamdunk really only supports NGM alignments due to the said requirement of certain BAM tags to...

What you could try is to crank the number of threads up even more - maybe to 30 and see if that helps. To help with the tags, could you...

Hi - sorry I was on retreat this week, so here's my answer: What biologists often want is any DEG analysis is one value per gene. To this end, even...

So you have two cells side by side where you perform SLAM-seq and one of them on top had a drug treatment correct? Do you know also the drug effect,...

In theory they should not, because the filtered TC read bam file contains exactly those reads upon we base our TCReadCounts quantification.

How do you quantify the reads from the TC read bam file?

Does that somehow filter flagged multimappers?

Hi @seb-mueller sorry for the long delay. I dont have it now at the back of my had, but if there is no option to supply a SNP directory with...

Hi @seb-mueller please by all means submit a PR, that would be very welcome. I guess why this was so far not an important factor for us is that we...