Tobias Neumann

Hm do you have some duplicate entries in there? Can you check? Also, can you share a few lines of the bed file so I could have a look what...

Yes that looks correct to me. I would also try to map only the first and second read separately and see if you see an increase in T>C reads in...

Hm that is indeed weird if it works for some but not for all. I second @jkobject I would probably need one of the filtered bam files to see what's...

Hi - it should work if you only run the map + filter steps. Alternatively, what I do is typically supplying bed files that cover all the different custom references...

Hi, what happens if you activate the slamdunk conda env and run ```ngm```. Is it installed and does it list a version? Also, if you install slamdunk via conda, what...

Can you also send the content of this file? `/net/ascratch/people/plgmmaslon/slurm_jobdir/11143159/tmp/tmph3r81hoa`

OK, then I would still need this file sorry `/net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/alleyoop/Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationrates_utr.csv`

Hm is the bed file having different chr prefixes than the reference fa?

Yes then this disconnect is the problem

You should then also have 0 counts in the tcount output files