Open mmaslon opened 1 month ago
Can you also send the content of this file? /net/ascratch/people/plgmmaslon/slurm_jobdir/11143159/tmp/tmph3r81hoa
Sure. _NF3 /net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/alleyoop/Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationratesutr.csv (sorry the file does not want to upload, so I pasted the content)
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
I see that this file has only 0 values - this must be it, but the conversions seem to be working, i.e. I do see the epxected rates for this sample Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_overallrates.pdf
Hm is the bed file having different chr prefixes than the reference fa?
just started looking at it,primary assembly just numbers, bed chr1 etc.
Yes then this disconnect is the problem
You should then also have 0 counts in the tcount output files
Hi again, I re-run slamdunk all with corrected UTR file. This created map, filter, snp folders and files allright, but I encountered a new problem now with the counts - all empty files. Attached error file, the script is essentially the same, the UTR file changed, but it worked fine for the upstream steps.. slamerr_280824.txt I would be grateful for any pointers..
Hm which command are you using? And are all files in the count folder empty? Because at least some processes finished
Hi there, I am trying to test utrrates tool on my data.
I used
alleyoop rates
OK, and it produced boxplot as expected. The code for your reference was:However, when I tried to run the uttrates on the same file using the following code:
I encountered the problem. Please see the error file for the script and log produced by the tool. Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationrates_utr.log alleyloop_err.txt
Could you please advise what the issue could be?