pkerbs

Hey Daniel, thanks for your response. All the input reads are 100bp long not 101. So it shouldn't do the forced trimming as you said. Just for testing, I have...

Hi Daniel, grepping for the read yielded this result: ``` @SRR5484560.3 HWI-ST942:51:C3CGDACXX:2:1101:1459:2183 length=100 ATTCATGCCACCGCTTACTATAAAGTGGACGACCCAGTGTGGAACATTCAAATTGCAAGGATGCTTGAGCTGCCCACTATCTACAGGAAAGTTTATNNNN +SRR5484560.3 HWI-ST942:51:C3CGDACXX:2:1101:1459:2183 length=100 ?@@FFFDEHHDFHIIGGDHGDHHII

Hey Daniel, this bug seems to be not only restricted to certain genes. Reported fusion events that have "SPOTLIGHT" in the "Fusion_finding_method" column all show wrong positions for the 3'...

Is there some progress on this? I agree that it would be very useful to access params in input and output section.

Hi Shuqi, thank you for your response. I tried that already, but unfortunately I still get the same error message: ``` × Getting requirements to build wheel did not run...

Hello Shuqi, I tried your suggestion and indeed it worked by installing PyVCF first in a freshly created virtual environment. What I did (with Python 3.9.5 installed): ``` python -m...

For anyone who is facing the same issue: The problem seems to be that I only want to plot "chr1" but I provide 'genome' and 'cytoband ' GRanges objects containing...

Ah yes, sorry, forgot to mention. I am using version 0.2.4

Hi @ArtRand, thank you very much for your quick assessment and your work on that. For now, I will use your recommendations then.

Hi Arthur, thank you for the clarification. I figured I could maybe achieve this by doing: ``` modkit extract calls \ --filter-threshold 0.85 \ --mod-thresholds m:0.85 \ --threads 16 \...