Example of how to generate junction file from fastq

[lukauskas]

I realise this is a bit beyond scope for proActiv but it would be helpful to have an example on how to generate a valid junction file from raw reads (using STAR or Tophat2/HISAT2 for instance) for completeness.

Would prevent people like me who now find themselves a bit lost in the docs for these aligners and wondering which options are needed and which are optional.

[jonathangoeke]

Hi @lukauskas it's a good idea, thanks for the suggestion. proActiv has no specific requirements (and it will actually work with any aligner, not just STAR and TopHat2 if you use bam). In any case it'll be good to provide a default command line, we will include this in the workflow.