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vpc-ccg / genion

GENe fusION
MIT License
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option to output metadata for the detected fusions #2

Closed shernadi closed 2 years ago

shernadi commented 2 years ago

Hi,

I have analysed some data using Genion lately and although the analysis finished quite smoothly I was wondering if there is an easy way to get Genion to include bit more details in the output table or maybe to a log file regarding the detected fusions? I think it would be quite useful to have some info on things such as supporting-read IDs, chromosome locations with position of the breakpoints in the genome to make the evaluation process a bit easier.

Many Thanks!

f0t1h commented 2 years ago

Thank you for the feedback. I will prepare an update to print detailed logs.

shernadi commented 2 years ago

Hi,

Thank you for including the additional data into the outputs so quickly, I found them really useful! I am not sure if it is related but I am experiencing sum issues when analysing the same samples with the new version though (interestingly only with some of the samples), where I am getting the following error: 

genion: src/annotate.cpp:204: void annotate::interval::extend(const annotate::interval&): Assertion `reverse_strand == other.reverse_strand' failed.
--

(I am using minimap2 to generate the alignments)

Many Thanks!

f0t1h commented 2 years ago

Can you let me know, which gene annotation are you using for the run? That error should only raise when a gene has exons on different strands. I will look in detail to see if it is something else.

f0t1h commented 2 years ago

OK, I forgot about palindromic reads when I put that assertion. I removed it in the latest update, since palindromic reads shouldn't raise any problems on the current breakpoint calculation. If you are using bioconda, it should update soon as well.