Hi Matt,
thanks for the reply.
The analysis is from a bachelor student but I think I found the correct build and delta psi shell-script:
He used the following commands:
majiq build /share/project/jonas/2/MAJIQ/gencode.v37.primary_assembly.annotation.gff3 -c /share/project/jonas/2/MAJIQ/MAJIQ.config -j 4 --minreads 20 --min-denovo 30 --min-intronic-cov 0.1 -o /share/project/jonas/2/MAJIQ/out
majiq deltapsi -grp1 "/share/project/jonas/2/MAJIQ/out/CT1-Aligned.sortedByCoord.out.majiq" "/share/project/jonas/2/MAJIQ/out/CT2-Aligned.sortedByCoord.out.majiq" "/share/project/jonas/2/MAJIQ/out/CT3-Aligned.sortedByCoord.out.majiq" -grp2 "/share/project/jonas/2/MAJIQ/out/KO1-Aligned.sortedByCoord.out.majiq" "/share/project/jonas/2/MAJIQ/out/KO2-Aligned.sortedByCoord.out.majiq" "/share/project/jonas/2/MAJIQ/out/KO3-Aligned.sortedByCoord.out.majiq" -j 4 --minreads 25 --prior-minreads 50 --output-type voila -o /share/project/jonas/2/MAJIQ -n A_CT A_KO
I think the first inclusion junction is an annotated one so --minreads is the parameter to look at. I am not really sure if I understand the parameter correctly but shouldn't the first inclusion junction survive this filtering step?
Best,
Mario